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Sample records for cellular interaction model

  1. Development and validation of computational models of cellular interaction

    OpenAIRE

    Smallwood, R H; Holcombe, W.M.L.; Walker, D C

    2004-01-01

    In this paper we take the view that computational models of biological systems should satisfy two conditions – they should be able to predict function at a systems biology level, and robust techniques of validation against biological models must be available. A modelling paradigm for developing a predictive computational model of cellular interaction is described, and methods of providing robust validation against biological models are explored, followed by a consideration of soft...

  2. Electromagnetic cellular interactions

    Czech Academy of Sciences Publication Activity Database

    Cifra, Michal; Fields, J. S.; Farhadi, A.

    2011-01-01

    Roč. 105, č. 3 (2011), 223-246. ISSN 0079-6107. [36th International Congress of Physiological Sciences (IUPS2009). Kyoto, 27.07.2009-01.08.2009] R&D Projects: GA ČR(CZ) GPP102/10/P454 Institutional research plan: CEZ:AV0Z20670512 Keywords : bioelectric phenomena * cellular biophysics Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 3.203, year: 2011

  3. Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson’s disease

    Science.gov (United States)

    Keane, Harriet; Ryan, Brent J.; Jackson, Brendan; Whitmore, Alan; Wade-Martins, Richard

    2015-11-01

    Neurodegenerative diseases are complex multifactorial disorders characterised by the interplay of many dysregulated physiological processes. As an exemplar, Parkinson’s disease (PD) involves multiple perturbed cellular functions, including mitochondrial dysfunction and autophagic dysregulation in preferentially-sensitive dopamine neurons, a selective pathophysiology recapitulated in vitro using the neurotoxin MPP+. Here we explore a network science approach for the selection of therapeutic protein targets in the cellular MPP+ model. We hypothesised that analysis of protein-protein interaction networks modelling MPP+ toxicity could identify proteins critical for mediating MPP+ toxicity. Analysis of protein-protein interaction networks constructed to model the interplay of mitochondrial dysfunction and autophagic dysregulation (key aspects of MPP+ toxicity) enabled us to identify four proteins predicted to be key for MPP+ toxicity (P62, GABARAP, GBRL1 and GBRL2). Combined, but not individual, knockdown of these proteins increased cellular susceptibility to MPP+ toxicity. Conversely, combined, but not individual, over-expression of the network targets provided rescue of MPP+ toxicity associated with the formation of autophagosome-like structures. We also found that modulation of two distinct proteins in the protein-protein interaction network was necessary and sufficient to mitigate neurotoxicity. Together, these findings validate our network science approach to multi-target identification in complex neurological diseases.

  4. CELLULAR INTERACTIONS MEDIATED BY GLYCONECTIDS

    Directory of Open Access Journals (Sweden)

    O.Popescu

    1999-01-01

    Full Text Available Cellular interactions involve many types of cell surface molecules and operate via homophilic and/or heterophilic protein-protein and protein-carbohydrate binding. Our investigations in different model-systems (marine invertebrates and mammals have provided direct evidence that a novel class of primordial proteoglycans, named by us gliconectins, can mediate cell adhesion via a new alternative molecular mechanism of polyvalent carbohydrate-carbohydrate binding. Biochemical characterization of isolated and purified glyconectins revealed the presence of specific carbohydrate structures, acidic glycans, different from classical glycosaminoglycans. Such acidic glycans of high molecular weight containing fucose, glucuronic or galacturonic acids, and sulfate groups, originally found in sponges and sea urchin embryos, may represent a new class of carbohydrate carcino-embryonal antigens in mice and humans. Such interactions between biological macromolecules are usually investigated by kinetic binding studies, calorimetric methods, X-ray diffraction, nuclear magnetic resonance, and other spectroscopic analyses. However, these methods do not supply a direct estimation of the intermolecular binding forces that are fundamental for the function of the ligand-receptor association. Recently, we have introduced atomic force microscopy to quantify the binding strength between cell adhesion proteoglycans. Measurement of binding forces intrinsic to cell adhesion proteoglycans is necessary to assess their contribution to the maintenance of the anatomical integrity of multicellular organisms. As a model, we selected the glyconectin 1, a cell adhesion proteoglycan isolated from the marine sponge Microciona prolifera. This glyconectin mediates in vivo cell recognition and aggregation via homophilic, species-specific, polyvalent, and calcium ion-dependent carbohydrate-carbohydrate interactions. Under physiological conditions, an adhesive force of up to 400 piconewtons

  5. Modelling for near-surface interaction of lithium ceramics and sweep-gas by use of cellular automation

    International Nuclear Information System (INIS)

    Tritium release from the lithium ceramics as a fusion reactor breeder material is strongly affected by the composition of the sweep-gas as result of its influences with the material's surface. The typical surface processes which play important roles are adsorption, desorption and interaction between vacancy site and the constituents of the sweep-gas. Among a large number of studies and models, yet it seems to be difficult to model the overall behaviour of those processes due to its complex time-transient nature. In the present work the coarse grained atomic simulation based on the Cellular Automaton (CA) is used to model the dynamics of near-surface interaction between Li2O surface and sweep-gas that is consisting of a noble gas, hydrogen gas and water vapour. (author)

  6. Modeling and cellular studies

    International Nuclear Information System (INIS)

    Testing the applicability of mathematical models with carefully designed experiments is a powerful tool in the investigations of the effects of ionizing radiation on cells. The modeling and cellular studies complement each other, for modeling provides guidance for designing critical experiments which must provide definitive results, while the experiments themselves provide new input to the model. Based on previous experimental results the model for the accumulation of damage in Chlamydomonas reinhardi has been extended to include various multiple two-event combinations. Split dose survival experiments have shown that models tested to date predict most but not all the observed behavior. Stationary-phase mammalian cells, required for tests of other aspects of the model, have been shown to be at different points in the cell cycle depending on how they were forced to stop proliferating. These cultures also demonstrate different capacities for repair of sublethal radiation damage

  7. Cellular structure in system of interacting particles

    OpenAIRE

    Lev, Bohdan

    2008-01-01

    The general description of formation the cellular structure in the system of interacting particles is proposed. Interactions between particles are presumably well-understood and the phase transition in which can be studied in the scale of particle resolution. We presented analytical results of possible cellular structures for suspension of colloidal particles, in system particles immersed in liquid crystal and gravitational system. We have shown that cellular structure formation can occur in ...

  8. Investigation of cellular and protein interactions with model self-assembled monolayer surfaces

    Science.gov (United States)

    Tegoulia, Vassiliki Apostolou

    Self-assembled monolayers (SAMs) of alkanethiolates on gold have been used to investigate the effect of substrate surface properties on bacterial and blood cell adhesion in the presence and absence of blood proteins. Protein adsorption and binding strength on SAMs as well as complement activation by these model surfaces were also studied. It is hoped that information gained, regarding factors that influence biological processes, will lead to strategies for designing materials and surfaces that specifically inhibit cell adhesion and protein adsorption. Single component SAMs of the general formula HS(CH2) 10X, where X = CH3, CH2OH. COOH and CH2(OCH 2CH2)3OH, and two component mixed SAMs created from binary solutions of HS(CH2), OCH3 and HS(CH 2)10CH2OH, were used. Adhesion was investigated under well-defined flow conditions. Adhesion was found to be higher for the hydrophobic methyl and minimal for the tri(ethyleneoxide) terminated SAM. Preincubation of the SAMs with fibrinogen led to an increase in cell adhesion for bacteria and a decrease for leukocyte adhesion. The effect of surface chemistry on protein adsorption was studied for three blood proteins, fibrinogen, fibronectin and albumin. Adsorption was found to be higher on the hydrophobic CH3 surface and lower but comparable for the other surfaces while proteins adsorbed strongly on all surfaces. SAMs were also used to evaluate complement activation by foreign surfaces. The hydroxyl rich SAMs were found to activate complement more significantly than the anionic carboxyl and the hydrophobic methyl terminated SAMs. A surface modification was introduced to incorporate a zwitterionic phosphorylcholine (PC) group on a hydroxyl monolayer in an effort to create a biomimetic surface that could minimize cell adhesion and protein adsorption. The good antifouling properties of the phosphorylcholine modified surface led to the synthesis of a novel phosphorylcholine functionalized thiol. Single component and two component

  9. Modelling cellular behaviour

    Science.gov (United States)

    Endy, Drew; Brent, Roger

    2001-01-01

    Representations of cellular processes that can be used to compute their future behaviour would be of general scientific and practical value. But past attempts to construct such representations have been disappointing. This is now changing. Increases in biological understanding combined with advances in computational methods and in computer power make it possible to foresee construction of useful and predictive simulations of cellular processes.

  10. Towards a continuum theory of movement in interacting cellular systems

    Science.gov (United States)

    Newman, Timothy

    2003-10-01

    Interacting cellular systems form the basis of all higher organisms, and are fundamental to the understanding of embryogenesis, organ function, and neoplasms. I will describe a stochastic model of cell interactions which can be applied to these problems, and present some of our recent results on chemotactic response.

  11. Predictive Modelling of Cellular Load

    OpenAIRE

    Carolan, Emmett; McLoone, Seamus; Farrell, Ronan

    2015-01-01

    This work examines the temporal dynamics of cellular load in four Irish regions. Large scale underutilisation of network resources is identified both at the regional level and at the level of individual cells. Cellular load is modeled and prediction intervals are generated. These prediction intervals are used to put an upper bound on usage in a particular cell at a particular time. Opportunities for improvements in network utilization by incorporating these upper bounds on usage are identifie...

  12. Systematic Cellular Disease Models Reveal Synergistic Interaction of Trisomy 21 and GATA1 Mutations in Hematopoietic Abnormalities.

    Science.gov (United States)

    Banno, Kimihiko; Omori, Sayaka; Hirata, Katsuya; Nawa, Nobutoshi; Nakagawa, Natsuki; Nishimura, Ken; Ohtaka, Manami; Nakanishi, Mahito; Sakuma, Tetsushi; Yamamoto, Takashi; Toki, Tsutomu; Ito, Etsuro; Yamamoto, Toshiyuki; Kokubu, Chikara; Takeda, Junji; Taniguchi, Hidetoshi; Arahori, Hitomi; Wada, Kazuko; Kitabatake, Yasuji; Ozono, Keiichi

    2016-05-10

    Chromosomal aneuploidy and specific gene mutations are recognized early hallmarks of many oncogenic processes. However, the net effect of these abnormalities has generally not been explored. We focused on transient myeloproliferative disorder (TMD) in Down syndrome, which is characteristically associated with somatic mutations in GATA1. To better understand functional interplay between trisomy 21 and GATA1 mutations in hematopoiesis, we constructed cellular disease models using human induced pluripotent stem cells (iPSCs) and genome-editing technologies. Comparative analysis of these engineered iPSCs demonstrated that trisomy 21 perturbed hematopoietic development through the enhanced production of early hematopoietic progenitors and the upregulation of mutated GATA1, resulting in the accelerated production of aberrantly differentiated cells. These effects were mediated by dosage alterations of RUNX1, ETS2, and ERG, which are located in a critical 4-Mb region of chromosome 21. Our study provides insight into the genetic synergy that contributes to multi-step leukemogenesis. PMID:27134169

  13. Dissecting stromal-epithelial interactions in a 3D in vitro cellularized intestinal model for permeability studies.

    Science.gov (United States)

    Pereira, Carla; Araújo, Francisca; Barrias, Cristina C; Granja, Pedro L; Sarmento, Bruno

    2015-07-01

    Absorption evaluation plays an increasingly important role at the early stage of drug discovery due to its potential to scan the ADME (absorption, distribution, metabolism and excretion) properties of new drug candidates. Therefore, a new three-dimensional (3D) in vitro model replicating the intestinal functioning is herein proposed aiming to dissect the stromal-epithelial interactions and evaluate the permeation of a model drug, insulin. Inspired on the intestinal mucosal architecture, the present model comprises intestinal myofibroblasts (CCD18-Co cells) embedded in Matrigel, onto which epithelial enterocytes (Caco-2 cells) and mucus-producing cells (HT29-MTX cells) were seeded. CCD18-Co myofibroblasts showed to have a central role in the remodeling of the surrounding matrix confirmed by the production of fibronectin. Subsequently, this matrix revealed to be essential to the maintenance of the model architecture by supporting the overlying epithelial cells. In terms of functionality, this model allowed the efficient prediction of insulin permeability in which the presence of mucus, the less tight character between Caco-2 and HT29-MTX epithelial cells and the 3D assembly were critical factors. Concluding, this model constitutes a robust tool in the drug development field with potential to bridge the traditional 2D cell culture models and in vivo animal models. PMID:25934277

  14. Cellular automata a parallel model

    CERN Document Server

    Mazoyer, J

    1999-01-01

    Cellular automata can be viewed both as computational models and modelling systems of real processes. This volume emphasises the first aspect. In articles written by leading researchers, sophisticated massive parallel algorithms (firing squad, life, Fischer's primes recognition) are treated. Their computational power and the specific complexity classes they determine are surveyed, while some recent results in relation to chaos from a new dynamic systems point of view are also presented. Audience: This book will be of interest to specialists of theoretical computer science and the parallelism challenge.

  15. Modeling In Vitro Cellular Responses to Silver Nanoparticles

    Directory of Open Access Journals (Sweden)

    Dwaipayan Mukherjee

    2014-01-01

    Full Text Available Engineered nanoparticles (NPs have been widely demonstrated to induce toxic effects to various cell types. In vitro cell exposure systems have high potential for reliable, high throughput screening of nanoparticle toxicity, allowing focusing on particular pathways while excluding unwanted effects due to other cells or tissue dosimetry. The work presented here involves a detailed biologically based computational model of cellular interactions with NPs; it utilizes measurements performed in human cell culture systems in vitro, to develop a mechanistic mathematical model that can support analysis and prediction of in vivo effects of NPs. The model considers basic cellular mechanisms including proliferation, apoptosis, and production of cytokines in response to NPs. This new model is implemented for macrophages and parameterized using in vitro measurements of changes in cellular viability and mRNA levels of cytokines: TNF, IL-1b, IL-6, IL-8, and IL-10. The model includes in vitro cellular dosimetry due to nanoparticle transport and transformation. Furthermore, the model developed here optimizes the essential cellular parameters based on in vitro measurements, and provides a “stepping stone” for the development of more advanced in vivo models that will incorporate additional cellular and NP interactions.

  16. Modeling cellular effects of coal pollutants

    International Nuclear Information System (INIS)

    The goal of this project is to develop and test models for the dose and dose-rate dependence of biological effects of coal pollutants on mammalian cells in tissue culture. Particular attention is given to the interaction of pollutants with the genetic material (deoxyribonucleic acid, or NDA) in the cell. Unlike radiation, which can interact directly with chromatin, chemical pollutants undergo numerous changes before the ultimate carcinogen becomes covalently bound to the DNA. Synthetic vesicles formed from a phospholipid bilayer are being used to investigate chemical transformations that may occur during the transport of pollutants across cellular membranes. The initial damage to DNA is rapidly modified by enzymatic repair systems in most living organisms. A model has been developed for predicting the effects of excision repair on the survival of human cells exposed to chemical carcinogens. In addition to the excision system, normal human cells also have tolerance mechanisms that permit continued growth and division of cells without removal of the damage. We are investigating the biological effect of damage passed to daughter cells by these tolerance mechanisms

  17. Understanding cisplatin resistance using cellular models.

    OpenAIRE

    STORDAL, BRITTA KRISTINA

    2007-01-01

    PUBLISHED Many mechanisms of cisplatin resistance have been proposed from studies of cellular models of resistance including changes in cellular drug accumulation, detoxification of the drug, inhibition of apoptosis and repair of the DNA adducts. A series of resistant models were developed from CCRF-CEM leukaemia cells with increasing doses of cisplatin from 100 ng/ml. This produced increasing resistance up to 7-fold with a treatment dose of 1.6 ?g/ml. Cisplatin resistance i...

  18. Understanding cisplatin resistance using cellular models

    OpenAIRE

    Stordal, Britta; Davey, Mary

    2007-01-01

    Many mechanisms of cisplatin resistance have been proposed from studies of cellular models of resistance including changes in cellular drug accumulation, detoxification of the drug, inhibition of apoptosis and repair of the DNA adducts. A series of resistant models were developed from CCRF-CEM leukaemia cells with increasing doses of cisplatin from 100 ng/ml. This produced increasing resistance up to 7-fold with a treatment dose of 1.6 microg/ml. Cisplatin resistance in these cells correlated...

  19. Modeling diffusion of innovations with probabilistic cellular automata

    OpenAIRE

    Boccara, Nino; Fuks, Henryk

    1997-01-01

    We present a family of one-dimensional cellular automata modeling the diffusion of an innovation in a population. Starting from simple deterministic rules, we construct models parameterized by the interaction range and exhibiting a second-order phase transition. We show that the number of individuals who eventually keep adopting the innovation strongly depends on connectivity between individuals.

  20. A cellular automata evacuation model considering friction and repulsion

    Institute of Scientific and Technical Information of China (English)

    SONG Weiguo; YU Yanfei; FAN Weicheng; Zhang Heping

    2005-01-01

    There exist interactions among pedestrians and between pedestrian and environment in evacuation. These interactions include attraction, repulsion and friction that play key roles in human evacuation behaviors, speed and efficiency. Most former evacuation models focus on the attraction force, while repulsion and friction are not well modeled. As a kind of multi-particle self-driven model, the social force model introduced in recent years can represent those three forces but with low simulation efficiency because it is a continuous model with complex rules. Discrete models such as the cellular automata model and the lattice gas model have simple rules and high simulation efficiency, but are not quite suitable for interactions' simulation. In this paper, a new cellular automata model based on traditional models is introduced in which repulsion and friction are modeled quantitatively. It is indicated that the model can simulate some basic behaviors, e.g.arching and the "faster-is-slower" phenomenon, in evacuation as multi-particle self-driven models, but with high efficiency as the normal cellular automata model and the lattice gas model.

  1. Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

    OpenAIRE

    Lin, Tien-ho; Bar-Joseph, Ziv; Murphy, Robert F.

    2011-01-01

    Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to m...

  2. Cellular Automaton Model for Immunology of Tumor Growth

    CERN Document Server

    Voitikova, M

    1998-01-01

    The stochastic discrete space-time model of an immune response on tumor spreading in a two-dimensional square lattice has been developed. The immunity-tumor interactions are described at the cellular level and then transferred into the setting of cellular automata (CA). The multistate CA model for system, in which all statesoflattice sites, composing of both immune and tumor cells populations, are the functions of the states of the 12 nearest neighbors. The CA model incorporates the essential featuresof the immunity-tumor system. Three regimes of neoplastic evolution including metastatic tumor growth and screen effect by inactive immune cells surrounding a tumor have been predicted.

  3. Animal and cellular models of human disease

    OpenAIRE

    Arends, Mark; White, Eric; Whitelaw, Christopher

    2016-01-01

    In this eighteenth (2016) Annual Review Issue of The Journal of Pathology, we present a collection of 19 invited review articles that cover different aspects of cellular and animal models of disease. These include genetically-engineered models, chemically-induced models, naturally-occurring models, and combinations thereof, with the focus on recent methodological and conceptual developments across a wide range of human diseases.

  4. A Modified Sensitive Driving Cellular Automaton Model

    Institute of Scientific and Technical Information of China (English)

    GE Hong-Xia; DAI Shi-Qiang; DONG Li-Yun; LEI Li

    2005-01-01

    A modified cellular automaton model for traffic flow on highway is proposed with a novel concept about the variable security gap. The concept is first introduced into the original Nagel-Schreckenberg model, which is called the non-sensitive driving cellular automaton model. And then it is incorporated with a sensitive driving NaSch model,in which the randomization brake is arranged before the deterministic deceleration. A parameter related to the variable security gap is determined through simulation. Comparison of the simulation results indicates that the variable security gap has different influence on the two models. The fundamental diagram obtained by simulation with the modified sensitive driving NaSch model shows that the maximumflow are in good agreement with the observed data, indicating that the presented model is more reasonable and realistic.

  5. A sub-cellular viscoelastic model for cell population mechanics.

    Directory of Open Access Journals (Sweden)

    Yousef Jamali

    Full Text Available Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes advantageous to use mathematical and 'in silico' (computational models as an alternate solution. This paper introduces a single-cell-based model representing the cross section of a typical tissue. Each cell in this model is an individual unit containing several sub-cellular elements, such as the elastic plasma membrane, enclosed viscoelastic elements that play the role of cytoskeleton, and the viscoelastic elements of the cell nucleus. The cell membrane is divided into segments where each segment (or point incorporates the cell's interaction and communication with other cells and its environment. The model is capable of simulating how cells cooperate and contribute to the overall structure and function of a particular tissue; it mimics many aspects of cellular behavior such as cell growth, division, apoptosis and polarization. The model allows for investigation of the biomechanical properties of cells, cell-cell interactions, effect of environment on cellular clusters, and how individual cells work together and contribute to the structure and function of a particular tissue. To evaluate the current approach in modeling different topologies of growing tissues in distinct biochemical conditions of the surrounding media, we model several key cellular phenomena, namely monolayer cell culture, effects of adhesion intensity, growth of epithelial cell through interaction with extra-cellular matrix (ECM, effects of a gap in the ECM, tensegrity and tissue morphogenesis and formation of hollow epithelial acini. The proposed computational model enables one to isolate the effects of biomechanical properties of individual cells and the

  6. Charged group surface accessibility determines micelleplexes formation and cellular interaction

    Science.gov (United States)

    Zhang, Yu; Liu, Yang; Sen, Soumyo; Král, Petr; Gemeinhart, Richard A.

    2015-04-01

    Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The model micelle system was formed from methoxy-poly(ethylene glycol)-b-poly(lactide) (mPEG-PLA) mixed with methoxy-poly(ethylene glycol)-b-poly(lactide)-b-oligoarginine (mPEG-PLA-Rx, x = 8 or 15). Surface properties of the micelles were varied by controlling the oligoarginine block length and conjugation density. Micelles were observed to have a core-shell conformation in the aqueous environment where the PLA block constituted the hydrophobic core, mPEG and oligoarginine formed a hydrophilic corona. Significantly different thermodynamic behaviors were observed during the interaction of single stranded miRNA with micelles of different surface properties, and the resulting micelleplexes mediated substantial cellular association. Depending upon the oligoarginine length and density, micelles exhibited miRNA loading capacity directly related to the presentation of charged groups on the surface. The effect of charged group accessibility of cationic micelle on micelleplex properties provides guidance on future miRNA delivery system design.Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The

  7. Imaging protein interactions in vivo with sub-cellular resolution

    CERN Document Server

    Raicu, Valerica; Fung, Russell; Melnichuk, Mike; Jansma, David B; Pisterzi, Luca; Fox, Michael; Wells, James W; Saldin, Dilano K

    2008-01-01

    Resonant Energy Transfer (RET) from an optically excited donor molecule (D) to a non-excited acceptor molecule (A) residing nearby is widely used to detect molecular interactions in living cells. Stoichiometric information, such as the number of proteins forming a complex, has been obtained so far for a handful of proteins, but only after exposing the sample sequentially to at least two different excitation wavelengths. During this lengthy process of measurement, the molecular makeup of a cellular region may change, and this has so far limited the applicability of RET to determination of cellular averages. Here we demonstrate a method for imaging protein complex distribution in living cells with sub-cellular spatial resolution, which relies on a spectrally-resolved two-photon microscope, a simple but competent theory, and a keen selection of fluorescent tags. This technology may eventually lead to tracking dynamics of macromolecular complex formation and dissociation with spatial resolution inside living cell...

  8. A Mathematical Model for Cisplatin Cellular Pharmacodynamics

    Directory of Open Access Journals (Sweden)

    Ardith W. El-Kareh

    2003-03-01

    Full Text Available A simple theoretical model for the cellular pharmacodynamics of cisplatin is presented. The model, which takes into account the kinetics of cisplatin uptake by cells and the intracellular binding of the drug, can be used to predict the dependence of survival (relative to controls on the time course of extracellular exposure. Cellular pharmacokinetic parameters are derived from uptake data for human ovarian and head and neck cancer cell lines. Survival relative to controls is assumed to depend on the peak concentration of DNA-bound intracellular platinum. Model predictions agree well with published data on cisplatin cytotoxicity for three different cancer cell lines, over a wide range of exposure times. In comparison with previously published mathematical models for anticancer drug pharmacodynamics, the present model provides a better fit to experimental data sets including long exposure times (∼100 hours. The model provides a possible explanation for the fact that cell kill correlates well with area under the extracellular concentration-time curve in some data sets, but not in others. The model may be useful for optimizing delivery schedules and for the dosing of cisplatin for cancer therapy.

  9. Cellular mechanisms underlying the interaction between cannabinoid and opioid system.

    Science.gov (United States)

    Parolaro, D; Rubino, T; Viganò, D; Massi, P; Guidali, C; Realini, N

    2010-04-01

    Recently, the presence of functional interaction between the opioid and cannabinoid system has been shown in various pharmacological responses. Although there is an increasing interest for the feasible therapeutic application of a co-administration of cannabinoids and opioids in some disorders (i.e. to manage pain, to modulate immune system and emotions) and the combined use of the two drugs by drug abusers is becoming largely diffuse, only few papers focused on cellular and molecular mechanisms underlying this interaction. This review updates the biochemical and molecular underpinnings of opioid and cannabinoid interaction, both within the central nervous system and periphery. The most convincing theory for the explanation of this reciprocal interaction involves (i) the release of opioid peptides by cannabinoids or endocannabinoids by opioids, (ii) the existence of a direct receptor-receptor interaction when the receptors are co-expressed in the same cells, and (iii) the interaction of their intracellular pathways. Finally, the cannabinoid/opioid interaction might be different in the brain rewarding networks and in those accounting for other pharmacological effects (antinociception, modulation of emotionality and cognitive behavior), as well as between the central nervous system and periphery. Further insights about the cannabinoid/opioid interaction could pave the way for new and promising therapeutic approaches. PMID:20017730

  10. Cellular automata modelling of hantarvirus infection

    International Nuclear Information System (INIS)

    Hantaviruses are a group of viruses which have been identified as being responsible for the outbreak of diseases such as the hantavirus pulmonary syndrome. In an effort to understand the characteristics and dynamics of hantavirus infection, mathematical models based on differential equations have been developed and widely studied. However, such models neglect the local characteristics of the spreading process and do not include variable susceptibility of individuals. In this paper, we develop an alternative approach based on cellular automata to analyze and study the spatiotemporal patterns of hantavirus infection.

  11. Cellular automata modelling of hantarvirus infection

    Energy Technology Data Exchange (ETDEWEB)

    Abdul Karim, Mohamad Faisal [School of Distance Education, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: faisal@usm.my; Md Ismail, Ahmad Izani [School of Mathematical Sciences, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: izani@cs.usm.my; Ching, Hoe Bee [School of Mathematical Sciences, Universiti Sains Malaysia, Minden 11800, Penang (Malaysia)], E-mail: Bee_Ching_Janice_Hoe@dell.com

    2009-09-15

    Hantaviruses are a group of viruses which have been identified as being responsible for the outbreak of diseases such as the hantavirus pulmonary syndrome. In an effort to understand the characteristics and dynamics of hantavirus infection, mathematical models based on differential equations have been developed and widely studied. However, such models neglect the local characteristics of the spreading process and do not include variable susceptibility of individuals. In this paper, we develop an alternative approach based on cellular automata to analyze and study the spatiotemporal patterns of hantavirus infection.

  12. Spatial game in cellular automaton evacuation model

    Science.gov (United States)

    von Schantz, Anton; Ehtamo, Harri

    2015-11-01

    For numerical simulations of crowd dynamics in an evacuation we need a computationally light environment, such as the cellular automaton model (CA). By choosing the right model parameters, different types of crowd behavior and collective effects can be produced. But the CA does not answer why, when, and how these different behaviors and collective effects occur. In this article, we present a model, where we couple a spatial evacuation game to the CA. In the game, an agent chooses its strategy by observing its neighbors' strategies. The game matrix changes with the distance to the exit as the evacuation conditions develop. In the resulting model, an agent's strategy choice alters the parameters that govern its behavior in the CA. Thus, with our model, we are able to simulate how evacuation conditions affect the behavior of the crowd. Also, we show that some of the collective effects observed in evacuations are a result of the simple game the agents play.

  13. Cellular interactions in the pathogenesis of interstitial lung diseases.

    Science.gov (United States)

    Bagnato, Gianluca; Harari, Sergio

    2015-03-01

    Interstitial lung disease (ILD) encompasses a large and diverse group of pathological conditions that share similar clinical, radiological and pathological manifestations, despite potentially having quite different aetiologies and comorbidities. Idiopathic pulmonary fibrosis (IPF) represents probably the most aggressive form of ILD and systemic sclerosis is a multiorgan fibrotic disease frequently associated with ILD. Although the aetiology of these disorders remains unknown, in this review we analyse the pathogenic mechanisms by cell of interest (fibroblast, fibrocyte, myofibroblast, endothelial and alveolar epithelial cells and immune competent cells). New insights into the complex cellular contributions and interactions will be provided, comparing the role of cell subsets in the pathogenesis of IPF and systemic sclerosis. PMID:25726561

  14. A cellular automata model for ant trails

    Indian Academy of Sciences (India)

    Sibel Gokce; Ozhan Kayacan

    2013-05-01

    In this study, the unidirectional ant traffic flow with U-turn in an ant trail was investigated using one-dimensional cellular automata model. It is known that ants communicate with each other by dropping a chemical, called pheromone, on the substrate. Apart from the studies in the literature, it was considered in the model that (i) ant colony consists of two kinds of ants, goodand poor-smelling ants, (ii) ants might make U-turn for some special reasons. For some values of densities of good- and poor-smelling ants, the flux and mean velocity of the colony were studied as a function of density and evaporation rate of pheromone.

  15. A cellular automaton model for tumor growth in heterogeneous environment

    Science.gov (United States)

    Jiao, Yang; Torquato, Sal

    2011-03-01

    Cancer is not a single disease: it exhibits heterogeneity on different spatial and temporal scales and strongly interacts with its host environment. Most mathematical modeling of malignant tumor growth has assumed a homogeneous host environment. We have developed a cellular automaton model for tumor growth that explicitly incorporates the structural heterogeneity of the host environment such as tumor stroma. We show that these structural heterogeneities have non-trivial effects on the tumor growth dynamics and prognosis. Y. J. is supported by PSOC, NCI.

  16. Investigation of cellular responses upon interaction with silver nanoparticles

    Directory of Open Access Journals (Sweden)

    Subbiah R

    2015-08-01

    Full Text Available Ramesh Subbiah,1,2 Seong Beom Jeon,3,4 Kwideok Park,1,2 Sang Jung Ahn,4,5 Kyusik Yun3 1Center for Biomaterials, Korea Institute of Science and Technology, Seoul, 2Department of Biomedical Engineering, Korea University of Science and Technology, Daejon, 3Department of Bionanotechnology, Gachon University, Gyeonggi-do, 4Centre for Advanced Instrumentation, Korea Research Institute of Standard and Science, 5Major of Nano Science, Korea University of Science and Technology, Daejeon, Republic of Korea Abstract: In order for nanoparticles (NPs to be applied in the biomedical field, a thorough investigation of their interactions with biological systems is required. Although this is a growing area of research, there is a paucity of comprehensive data in cell-based studies. To address this, we analyzed the physicomechanical responses of human alveolar epithelial cells (A549, mouse fibroblasts (NIH3T3, and human bone marrow stromal cells (HS-5, following their interaction with silver nanoparticles (AgNPs. When compared with kanamycin, AgNPs exhibited moderate antibacterial activity. Cell viability ranged from ≤80% at a high AgNPs dose (40 µg/mL to >95% at a low dose (10 µg/mL. We also used atomic force microscopy-coupled force spectroscopy to evaluate the biophysical and biomechanical properties of cells. This revealed that AgNPs treatment increased the surface roughness (P<0.001 and stiffness (P<0.001 of cells. Certain cellular changes are likely due to interaction of the AgNPs with the cell surface. The degree to which cellular morphology was altered directly proportional to the level of AgNP-induced cytotoxicity. Together, these data suggest that atomic force microscopy can be used as a potential tool to develop a biomechanics-based biomarker for the evaluation of NP-dependent cytotoxicity and cytopathology. Keywords: AFM, roughness, nanoindentation, biomarker, cytotoxicity, biomechanics

  17. Modeling the topological organization of cellular processes.

    Science.gov (United States)

    Giavitto, Jean-Louis; Michel, Olivier

    2003-07-01

    The cell as a dynamical system presents the characteristics of having a dynamical structure. That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state. This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation. In this context, the goal of the MGS project is to develop an experimental programming language dedicated to the simulation of this kind of systems. MGS proposes a unified view on several computational mechanisms (CHAM, Lindenmayer systems, Paun systems, cellular automata) enabling the specification of spatially localized computations on heterogeneous entities. The evolution of a dynamical structure is handled through the concept of transformation which relies on the topological organization of the system components. An example based on the modeling of spatially distributed biochemical networks is used to illustrate how these notions can be used to model the spatial and temporal organization of intracellular processes. PMID:12915272

  18. Cellular automata modelling of biomolecular networks dynamics.

    Science.gov (United States)

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  19. Cellular interactions in the pathogenesis of interstitial lung diseases

    Directory of Open Access Journals (Sweden)

    Gianluca Bagnato

    2015-03-01

    Full Text Available Interstitial lung disease (ILD encompasses a large and diverse group of pathological conditions that share similar clinical, radiological and pathological manifestations, despite potentially having quite different aetiologies and comorbidities. Idiopathic pulmonary fibrosis (IPF represents probably the most aggressive form of ILD and systemic sclerosis is a multiorgan fibrotic disease frequently associated with ILD. Although the aetiology of these disorders remains unknown, in this review we analyse the pathogenic mechanisms by cell of interest (fibroblast, fibrocyte, myofibroblast, endothelial and alveolar epithelial cells and immune competent cells. New insights into the complex cellular contributions and interactions will be provided, comparing the role of cell subsets in the pathogenesis of IPF and systemic sclerosis.

  20. Cellular automata modeling of cooperative eutectic growth

    Directory of Open Access Journals (Sweden)

    E. Olejnik

    2010-01-01

    Full Text Available The model and results of the 2D simulation of the cooperative growth of two phases in the lamellar eutectic are presented. The pro-posed model takes into account heat transfer, components diffusion and nonstationary concentration distribution in the liquid and solid phases, non-equlibrium nature of the phase transformation and kinetics of the growth, influence of the surface energy and interface curva-ture on the conditions of the thermodynamic equilibrium. For the determination of the phase interface shape the Cellular Automata tech-nique (CA was used. For the calculation of temperature and concentration distribution the numerical solution of the Fourier equation was used. The partial differential equations were solved by Finite Differences Method (FDM. The spatial position and cell sizes of CA lattice and FDM mesh are equal.Proposed model can predict the steady state growth with a constant interlamellar spacing in the regular plate eutectic, as well as some transient processes that bring to the changes of that parameters. Obtained simulation data show the solid-liquid interface changes result in the termination of lamella and enlargement of interlamellar spacing. Another simulation results illustrate a pocket formation in the center of one phase that forestalls nucleation (or intergrowth of the new lamellae of another phase. The data of the solidification study of the transparent material (CBr4 – 8,4% C2Cl6 obtained in the thin layer demonstrate the qualita-tive agreement of the simulation.

  1. Motor Schema-Based Cellular Automaton Model for Pedestrian Dynamics

    Science.gov (United States)

    Weng, Wenguo; Hasemi, Yuji; Fan, Weicheng

    A new cellular automaton model for pedestrian dynamics based on motor schema is presented. Each pedestrian is treated as an intelligent mobile robot, and motor schemas including move-to-goal, avoid-away and avoid-around drive pedestrians to interact with their environment. We investigate the phenomenon of many pedestrians with different move velocities escaping from a room. The results show that the pedestrian with high velocity have predominance in competitive evacuation, if we only consider repulsion from or avoiding around other pedestrians, and interaction with each other leads to disordered evacuation, i.e., decreased evacuation efficiency. Extensions of the model using learning algorithms for controlling pedestrians, i.e., reinforcement learning, neural network and genetic algorithms, etc. are noted.

  2. Analytical Modeling of Uplink Cellular Networks

    CERN Document Server

    Novlan, Thomas D; Andrews, Jeffrey G

    2012-01-01

    Cellular uplink analysis has typically been undertaken by either a simple approach that lumps all interference into a single deterministic or random parameter in a Wyner-type model, or via complex system level simulations that often do not provide insight into why various trends are observed. This paper proposes a novel middle way that is both accurate and also results in easy-to-evaluate integral expressions based on the Laplace transform of the interference. We assume mobiles and base stations are randomly placed in the network with each mobile pairing up to its closest base station. The model requires two important changes compared to related recent work on the downlink. First, dependence is introduced between the user and base station point processes to make sure each base station serves a single mobile in the given resource block. Second, per-mobile power control is included, which further couples the locations of the mobiles and their receiving base stations. Nevertheless, we succeed in deriving the cov...

  3. Integrated cellular network of transcription regulations and protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2010-03-01

    Full Text Available Abstract Background With the accumulation of increasing omics data, a key goal of systems biology is to construct networks at different cellular levels to investigate cellular machinery of the cell. However, there is currently no satisfactory method to construct an integrated cellular network that combines the gene regulatory network and the signaling regulatory pathway. Results In this study, we integrated different kinds of omics data and developed a systematic method to construct the integrated cellular network based on coupling dynamic models and statistical assessments. The proposed method was applied to S. cerevisiae stress responses, elucidating the stress response mechanism of the yeast. From the resulting integrated cellular network under hyperosmotic stress, the highly connected hubs which are functionally relevant to the stress response were identified. Beyond hyperosmotic stress, the integrated network under heat shock and oxidative stress were also constructed and the crosstalks of these networks were analyzed, specifying the significance of some transcription factors to serve as the decision-making devices at the center of the bow-tie structure and the crucial role for rapid adaptation scheme to respond to stress. In addition, the predictive power of the proposed method was also demonstrated. Conclusions We successfully construct the integrated cellular network which is validated by literature evidences. The integration of transcription regulations and protein-protein interactions gives more insight into the actual biological network and is more predictive than those without integration. The method is shown to be powerful and flexible and can be used under different conditions and for different species. The coupling dynamic models of the whole integrated cellular network are very useful for theoretical analyses and for further experiments in the fields of network biology and synthetic biology.

  4. Nanoparticle-cell interactions: molecular structure of the protein corona and cellular outcomes.

    Science.gov (United States)

    Fleischer, Candace C; Payne, Christine K

    2014-08-19

    The use of nanoparticles (NPs) in biology and medicine requires a molecular-level understanding of how NPs interact with cells in a physiological environment. A critical difference between well-controlled in vitro experiments and in vivo applications is the presence of a complex mixture of extracellular proteins. It has been established that extracellular serum proteins present in blood will adsorb onto the surface of NPs, forming a "protein corona". Our goal was to understand how this protein layer affected cellular-level events, including NP binding, internalization, and transport. A combination of microscopy, which provides spatial resolution, and spectroscopy, which provides molecular information, is necessary to probe protein-NP-cell interactions. Initial experiments used a model system composed of polystyrene NPs functionalized with either amine or carboxylate groups to provide a cationic or anionic surface, respectively. Serum proteins adsorb onto the surface of both cationic and anionic NPs, forming a net anionic protein-NP complex. Although these protein-NP complexes have similar diameters and effective surface charges, they show the exact opposite behavior in terms of cellular binding. In the presence of bovine serum albumin (BSA), the cellular binding of BSA-NP complexes formed from cationic NPs is enhanced, whereas the cellular binding of BSA-NP complexes formed from anionic NPs is inhibited. These trends are independent of NP diameter or cell type. Similar results were obtained for anionic quantum dots and colloidal gold nanospheres. Using competition assays, we determined that BSA-NP complexes formed from anionic NPs bind to albumin receptors on the cell surface. BSA-NP complexes formed from cationic NPs are redirected to scavenger receptors. The observation that similar NPs with identical protein corona compositions bind to different cellular receptors suggested that a difference in the structure of the adsorbed protein may be responsible for the

  5. Cellular automaton model of coupled mass transport and chemical reactions

    International Nuclear Information System (INIS)

    Mass transport, coupled with chemical reactions, is modelled as a cellular automaton in which solute molecules perform a random walk on a lattice and react according to a local probabilistic rule. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. The model is applied to the reactions a + b ↔c and a + b →c, where we observe interesting macroscopic effects resulting from microscopic fluctuations and spatial correlations between molecules. We also simulate autocatalytic reaction schemes displaying spontaneous formation of spatial concentration patterns. Finally, we propose and discuss the limitations of a simple model for mineral-solute interaction. (author) 5 figs., 20 refs

  6. Global Network Model based on Earth Grid and Cellular

    Directory of Open Access Journals (Sweden)

    Dongqi Lu

    2014-06-01

    Full Text Available We aim to understand the current health state of the Earth and find how human activities influence it. Based on the theory of Earth’s Grid and Cellular Automata, we define and test a global network model, analyze the mutual interactions and feedbacks of ecosystem, hydrologic circle and atmosphere. In addition, we consult a lot of data to find a benchmark for the “Earth Health Map”, with the ecosystem distribution on it, which can be helpful for making a strategic decision for policy makers and prediction. Our model can be extended to other similar fields. In the end, we discuss the sensitivity of parameters selection, and the superiorities and weaknesses of our model.

  7. Thymocyte migration: an affair of multiple cellular interactions?

    Directory of Open Access Journals (Sweden)

    Savino W.

    2003-01-01

    Full Text Available Cell migration is a crucial event in the general process of thymocyte differentiation. The cellular interactions involved in the control of this migration are beginning to be defined. At least chemokines and extracellular matrix proteins appear to be part of the game. Cells of the thymic microenvironment produce these two groups of molecules, whereas developing thymocytes express the corresponding receptors. Moreover, although chemokines and extracellular matrix can drive thymocyte migration per se, a combined role for these molecules appears to contribute to the resulting migration patterns of thymocytes in their various stages of differentiation. The dynamics of chemokine and extracellular matrix production and degradation is not yet well understood. However, matrix metalloproteinases are likely to play a role in the breakdown of intrathymic extracellular matrix contents. Thus, the physiological migration of thymocytes should be envisioned as a resulting vector of multiple, simultaneous and/or sequential stimuli involving chemokines, adhesive and de-adhesive extracellular matrix proteins, as well as matrix metalloproteinases. Accordingly, it is conceivable that any pathological change in any of these loops may result in the alteration of normal thymocyte migration. This seems to be the case in murine infection by the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas' disease. A better knowledge of the physiological mechanisms governing thymocyte migration will provide new clues for designing therapeutic strategies targeting developing T cells.

  8. Effects of multiple enzyme–substrate interactions in basic units of cellular signal processing

    International Nuclear Information System (INIS)

    Covalent modification cycles are a ubiquitous feature of cellular signalling networks. In these systems, the interaction of an active enzyme with the unmodified form of its substrate is essential for signalling to occur. However, this interaction is not necessarily the only enzyme–substrate interaction possible. In this paper, we analyse the behaviour of a basic model of signalling in which additional, non-essential enzyme–substrate interactions are possible. These interactions include those between the inactive form of an enzyme and its substrate, and between the active form of an enzyme and its product. We find that these additional interactions can result in increased sensitivity and biphasic responses, respectively. The dynamics of the responses are also significantly altered by the presence of additional interactions. Finally, we evaluate the consequences of these interactions in two variations of our basic model, involving double modification of substrate and scaffold-mediated signalling, respectively. We conclude that the molecular details of protein–protein interactions are important in determining the signalling properties of enzymatic signalling pathways. (paper)

  9. Fluctuation in option pricing using cellular automata based market models

    Science.gov (United States)

    Gao, Yuying; Beni, Gerardo

    2005-05-01

    A new agent-based Cellular Automaton (CA) computational algorithm for option pricing is proposed. CAs have been extensively used in modeling complex dynamical systems but not in modeling option prices. Compared with traditional tools, which rely on guessing volatilities to calculate option prices, the CA model is directly addressing market mechanisms and simulates price fluctuation from aggregation of actions made by interacting individual market makers in a large population. This paper explores whether CA models can provide reasonable good answers to pricing European options. The Black-Scholes model and the Binomial Tree model are used for comparison. Comparison reveals that CA models perform reasonably well in pricing options, reproducing overall characteristics of random walk based model, while at the same time providing plausible results for the 'fat-tail' phenomenon observed in many markets. We also show that the binomial tree model can be obtained from a CA rule. Thus, CA models are suitable tools to generalize the standard theories of option pricing.

  10. Critical Behavior in a Cellular Automata Animal Disease Transmission Model

    CERN Document Server

    Morley, P D; Chang, Julius

    2003-01-01

    Using a cellular automata model, we simulate the British Government Policy (BGP) in the 2001 foot and mouth epidemic in Great Britain. When clinical symptoms of the disease appeared on a farm, there is mandatory slaughter (culling) of all livestock on an infected premise (IP). Those farms that neighbor an IP (contiguous premise, CP), are also culled, aka nearest neighbor interaction. Farms where the disease may be prevalent from animal, human, vehicle or airborne transmission (dangerous contact, DC), are additionally culled, aka next-to-nearest neighbor iteractions and lightning factor. The resulting mathematical model possesses a phase transition, whereupon if the physical disease transmission kernel exceeds a critical value, catastrophic loss of animals ensues. The non-local disease transport probability can be as low as .01% per day and the disease can still be in the high mortality phase. We show that the fundamental equation for sustainable disease transport is the criticality equation for neutron fissio...

  11. Typhoid fever as cellular microbiological model

    OpenAIRE

    Andrade Dahir Ramos de; Andrade Júnior Dahir Ramos de

    2003-01-01

    The knowledge about typhoid fever pathogenesis is growing in the last years, mainly about the cellular and molecular phenomena that are responsible by clinical manifestations of this disease. In this article are discussed several recent discoveries, as follows: a) Bacterial type III protein secretion system; b) The five virulence genes of Salmonella spp. that encoding Sips (Salmonella invasion protein) A, B, C, D and E, which are capable of induce apoptosis in macrophages; c) The function of ...

  12. A cellular automata-based mathematical model for thymocyte development.

    Directory of Open Access Journals (Sweden)

    Hallan Souza-e-Silva

    Full Text Available Intrathymic T cell development is an important process necessary for the normal formation of cell-mediated immune responses. Importantly, such a process depends on interactions of developing thymocytes with cellular and extracellular elements of the thymic microenvironment. Additionally, it includes a series of oriented and tunely regulated migration events, ultimately allowing mature cells to cross endothelial barriers and leave the organ. Herein we built a cellular automata-based mathematical model for thymocyte migration and development. The rules comprised in this model take into account the main stages of thymocyte development, two-dimensional sections of the normal thymic microenvironmental network, as well as the chemokines involved in intrathymic cell migration. Parameters of our computer simulations with further adjusted to results derived from previous experimental data using sub-lethally irradiated mice, in which thymus recovery can be evaluated. The model fitted with the increasing numbers of each CD4/CD8-defined thymocyte subset. It was further validated since it fitted with the times of permanence experimentally ascertained in each CD4/CD8-defined differentiation stage. Importantly, correlations using the whole mean volume of young normal adult mice revealed that the numbers of cells generated in silico with the mathematical model fall within the range of total thymocyte numbers seen in these animals. Furthermore, simulations made with a human thymic epithelial network using the same mathematical model generated similar profiles for temporal evolution of thymocyte developmental stages. Lastly, we provided in silico evidence that the thymus architecture is important in the thymocyte development, since changes in the epithelial network result in different theoretical profiles for T cell development/migration. This model likely can be used to predict thymocyte evolution following therapeutic strategies designed for recovery of the

  13. A cellular automaton model for neurogenesis in Drosophila

    Science.gov (United States)

    Luthi, Pascal O.; Chopard, Bastien; Preiss, Anette; Ramsden, Jeremy J.

    1998-07-01

    A cellular automaton (CA) is constructed for the formation of the central nervous system of the Drosophila embryo. This is an experimentally well-studied system in which complex interactions between neighbouring cells appear to drive their differentiation into different types. It appears that all the cells initially have the potential to become neuroblasts, and all strive to this end, but those which differentiate first block their as yet undifferentiated neighbours from doing so. The CA makes use of observational evidence for a lateral inhibition mechanism involving signalling products S of the ‘proneural’ or neuralizing genes. The key concept of the model is that cells are continuously producing S, but the production rate is lowered by inhibitory signals received from neighbouring cells which have advanced further along the developmental pathway. Comparison with experimental data shows that it well accounts for the observed proportion of neuroectodermal cells delaminating as neuroblasts.

  14. Typhoid fever as cellular microbiological model

    Directory of Open Access Journals (Sweden)

    Andrade Dahir Ramos de

    2003-01-01

    Full Text Available The knowledge about typhoid fever pathogenesis is growing in the last years, mainly about the cellular and molecular phenomena that are responsible by clinical manifestations of this disease. In this article are discussed several recent discoveries, as follows: a Bacterial type III protein secretion system; b The five virulence genes of Salmonella spp. that encoding Sips (Salmonella invasion protein A, B, C, D and E, which are capable of induce apoptosis in macrophages; c The function of Toll R2 and Toll R4 receptors present in the macrophage surface (discovered in the Drosophila. The Toll family receptors are critical in the signalizing mediated by LPS in macrophages in association with LBP and CD14; d The lines of immune defense between intestinal lumen and internal organs; e The fundamental role of the endothelial cells in the inflammatory deviation from bloodstream into infected tissues by bacteria. In addition to above subjects, the authors comment the correlation between the clinical features of typhoid fever and the cellular and molecular phenomena of this disease, as well as the therapeutic consequences of this knowledge.

  15. Typhoid fever as cellular microbiological model.

    Science.gov (United States)

    de Andrade, Dahir Ramos; de Andrade Júnior, Dahir Ramos

    2003-01-01

    The knowledge about typhoid fever pathogenesis is growing in the last years, mainly about the cellular and molecular phenomena that are responsible by clinical manifestations of this disease. In this article are discussed several recent discoveries, as follows: a) Bacterial type III protein secretion system; b) The five virulence genes of Salmonella spp. that encoding Sips (Salmonella invasion protein) A, B, C, D and E, which are capable of induce apoptosis in macrophages; c) The function of Toll R2 and Toll R4 receptors present in the macrophage surface (discovered in the Drosophila). The Toll family receptors are critical in the signalizing mediated by LPS in macrophages in association with LBP and CD14; d) The lines of immune defense between intestinal lumen and internal organs; e) The fundamental role of the endothelial cells in the inflammatory deviation from bloodstream into infected tissues by bacteria. In addition to above subjects, the authors comment the correlation between the clinical features of typhoid fever and the cellular and molecular phenomena of this disease, as well as the therapeutic consequences of this knowledge. PMID:14502344

  16. TRAFFIC FLOW MODEL BASED ON CELLULAR AUTOMATION WITH ADAPTIVE DECELERATION

    OpenAIRE

    Shinkarev, A. A.

    2016-01-01

    This paper describes continuation of the authors’ work in the field of traffic flow mathematical models based on the cellular automata theory. The refactored representation of the multifactorial traffic flow model based on the cellular automata theory is used for a representation of an adaptive deceleration step implementation. The adaptive deceleration step in the case of a leader deceleration allows slowing down smoothly but not instantly. Concepts of the number of time steps without confli...

  17. Study of phase separation using liquid-gas model of lattice-gas cellular automata

    International Nuclear Information System (INIS)

    This report describes the study of phase separation by the liquid gas model of lattice gas cellular automata. The lattice gas cellular automaton is one model for simulating fluid phenomena which was proposed by Frisch, Hasslacher and Pomeau in 1986. In 1990, Appert and Zaleski added a new long-range interaction to lattice gas cellular automata to construct a model, the liquid-gas model, which could simulate phase separation using lattice-gas cellular automata. Gerits et al formulated the liquid-gas model mathematically using the theory of statistical dynamics in 1993 and explained the mechanism of phase separation in the liquid-gas model using the equation of state. At first this report explains the FHP model of lattice gas cellular automata and derives fluid dynamics equations such as the equation of continuity and the Navier-Stokes equation. Then the equation of state for the liquid-gas model which was derived by Gerits et al is modified by adding the interactions which were proposed by Appert but not considered by Gerits et al. The modified equation of state is verified by the computer simulation using the liquid gas model. The relation between phase separation and the equation of state is discussed. (author)

  18. Mapping of cellular iron using hyperspectral fluorescence imaging in a cellular model of Parkinson's disease

    Science.gov (United States)

    Oh, Eung Seok; Heo, Chaejeong; Kim, Ji Seon; Lee, Young Hee; Kim, Jong Min

    2013-05-01

    Parkinson's disease (PD) is characterized by progressive dopaminergic cell loss in the substantianigra (SN) and elevated iron levels demonstrated by autopsy and with 7-Tesla magnetic resonance imaging. Direct visualization of iron with live imaging techniques has not yet been successful. The aim of this study is to visualize and quantify the distribution of cellular iron using an intrinsic iron hyperspectral fluorescence signal. The 1-methyl-4-phenylpyridinium (MPP+)-induced cellular model of PD was established in SHSY5Y cells. The cells were exposed to iron by treatment with ferric ammonium citrate (FAC, 100 μM) for up to 6 hours. The hyperspectral fluorescence imaging signal of iron was examined usinga high- resolution dark-field optical microscope system with signal absorption for the visible/ near infrared (VNIR) spectral range. The 6-hour group showed heavy cellular iron deposition compared with the small amount of iron accumulation in the 1-hour group. The cellular iron was dispersed in a small, particulate form, whereas extracellular iron was detected in an aggregated form. In addition, iron particles were found to be concentrated on the cell membrane/edge of shrunken cells. The cellular iron accumulation readily occurred in MPP+-induced cells, which is consistent with previous studies demonstrating elevated iron levels in the SN in PD. This direct iron imaging methodology could be applied to analyze the physiological role of iron in PD, and its application might be expanded to various neurological disorders involving other metals, such as copper, manganese or zinc.

  19. Cellular automaton for realistic modelling of landslides

    Directory of Open Access Journals (Sweden)

    E. Segre

    1995-01-01

    Full Text Available A numerical model is developed for the simulation of debris flow in landslides over a complex three dimensional topography. The model is then validated by comparing a simulation with reported field data. Our model is in fact a realistic elaboration of simpler "sandpile automata", which have in recent years been studied as supposedly paradigmatic of "self-organized criticality". Statistics and scaling properties of the simulation are examined, and show that the model has an intermittent behaviour.

  20. Body composition analysis: Cellular level modeling of body component ratios

    OpenAIRE

    Z. Wang; Heymsfield, S. B.; PI-SUNYER, F.X.; Gallagher, D.; PIERSON, R.N.

    2008-01-01

    During the past two decades, a major outgrowth of efforts by our research group at St. Luke’s-Roosevelt Hospital is the development of body composition models that include cellular level models, models based on body component ratios, total body potassium models, multi-component models, and resting energy expenditure-body composition models. This review summarizes these models with emphasis on component ratios that we believe are fundamental to understanding human body composition during growt...

  1. From cellular to tissue scales by asymptotic limits of thermostatted kinetic models

    Science.gov (United States)

    Bianca, Carlo; Dogbe, Christian; Lemarchand, Annie

    2016-02-01

    Tumor growth strictly depends on the interactions occurring at the cellular scale. In order to obtain the linking between the dynamics described at tissue and cellular scales, asymptotic methods have been employed, consisting in deriving tissue equations by suitable limits of mesoscopic models. In this paper, the evolution at the cellular scale is described by thermostatted kinetic theory that include conservative, nonconservative (proliferation, destruction and mutations), stochastic terms, and the role of external agents. The dynamics at the tissue scale (cell-density evolution) is obtained by performing a low-field scaling and considering the related convergence of the rescaled framework when the scaling parameter goes to zero.

  2. Cellular mechanisms regulating sperm-zona pellucida interaction

    Institute of Scientific and Technical Information of China (English)

    Andrew T Reid; Kate Redgrove; R John Aitken; Brett Nixon

    2011-01-01

    For mammalian spermatozoa to exhibit the ability to bind the zona pellucida(ZP)they must undergo three distinct phases of maturation,namely,spermatogenesis(testis),epididymal maturation(epididymis)and capacitation(female reproductive tract).An impressive array of spermatozoa surface remodeling events accompany these phases of maturation and appear critical for recognition and adhesion of the outer vestments of the oocyte,a structure known as the ZP.It is becoming increasingly apparent that species-specific zona adhesion is not mediated by a single receptor.Instead,compelling evidence now points toward models implicating a multiplicity of receptor-ligand interactions.This notion is in keeping with emerging research that has shown that there is a dynamic aggregation of proteins believed to be important in sperm-ZP recognition to the regions of sperm that mediate this binding event.Such remodeling may in turn facilitate the assembly of a multimeric zona recognition complex(MZRC).Though formation of MZRCs raises questions regarding the nature of the block to polyspermy,formation and assembly of such a structure would no doubt explain the strenuous maturation process that sperm endure on their sojourn to functional maturity.

  3. Use of specific glycosidases to probe cellular interactions in the sea urchin embryo.

    Science.gov (United States)

    Idoni, Brian; Ghazarian, Haike; Metzenberg, Stan; Hutchins-Carroll, Virginia; Oppenheimer, Steven B; Carroll, Edward J

    2010-08-01

    We present an unusual and novel model for initial investigations of a putative role for specifically conformed glycans in cellular interactions. We have used alpha- and ss-amylase and alpha- and ss-glucosidase in dose-response experiments evaluating their effects on archenteron organization using the NIH designated sea urchin embryo model. In quantitative dose-response experiments, we show that defined activity levels of alpha-glucosidase and ss-amylase inhibited archenteron organization in living Lytechinus pictus gastrula embryos, whereas all concentrations of ss-glucosidase and alpha-amylase were without substantial effects on development. Product inhibition studies suggested that the enzymes were acting by their specific glycosidase activities and polyacrylamide gel electrophoresis suggested that there was no detectable protease contamination in the active enzyme samples. The results provide evidence for a role of glycans in sea urchin embryo cellular interactions with special reference to the possible structural conformation of these glycans based on the differential activities of the alpha- and ss-glycosidases. PMID:20435035

  4. Modeling cellular deformations using the level set formalism

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2008-07-01

    Full Text Available Abstract Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM, in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiration and show how this viscoelastic model can be incorporated into LSM simulations to recreate the observed protrusion of cells into the micropipette faithfully. We also demonstrate the use of our techniques by simulating the cell shape changes elicited by the chemotactic response to an external chemoattractant gradient. Conclusion Our results provide a simple but effective means of incorporating cellular deformations into mathematical simulations of cell signaling. Such methods will be useful for simulating important cellular events such as chemotaxis and cytokinesis.

  5. Computational model of cellular metabolic dynamics

    DEFF Research Database (Denmark)

    Li, Yanjun; Solomon, Thomas; Haus, Jacob M;

    2010-01-01

    Identifying the mechanisms by which insulin regulates glucose metabolism in skeletal muscle is critical to understanding the etiology of insulin resistance and type 2 diabetes. Our knowledge of these mechanisms is limited by the difficulty of obtaining in vivo intracellular data. To quantitatively...... cytosol and mitochondria. The model simulated skeletal muscle metabolic responses to insulin corresponding to human hyperinsulinemic-euglycemic clamp studies. Insulin-mediated rate of glucose disposal was the primary model input. For model validation, simulations were compared with experimental data...... type 2 diabetes....

  6. Modeling cellular deformations using the level set formalism

    OpenAIRE

    Yang Liu; Effler Janet C; Kutscher Brett L; Sullivan Sarah E; Robinson Douglas N; Iglesias Pablo A

    2008-01-01

    Abstract Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM), in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiratio...

  7. Cellular automata modeling of cooperative eutectic growth

    OpenAIRE

    E. Olejnik; E. Fraś; D. Gurgul; A. Burbelko

    2010-01-01

    The model and results of the 2D simulation of the cooperative growth of two phases in the lamellar eutectic are presented. The pro-posed model takes into account heat transfer, components diffusion and nonstationary concentration distribution in the liquid and solid phases, non-equlibrium nature of the phase transformation and kinetics of the growth, influence of the surface energy and interface curva-ture on the conditions of the thermodynamic equilibrium. For the determination of the phase ...

  8. Thrombospondin-1 Interacts with Trypanosoma cruzi Surface Calreticulin to Enhance Cellular Infection

    OpenAIRE

    Johnson, Candice A.; Kleshchenko, Yulia Y.; Ikejiani, Adaeze O.; Udoko, Aniekanabasi N.; Cardenas, Tatiana C.; Pratap, Siddharth; Duquette, Mark A.; Lima, Maria F.; Lawler, Jack; Villalta, Fernando; Nde, Pius N.

    2012-01-01

    Trypanosoma cruzi causes Chagas disease, which is a neglected tropical disease that produces severe pathology and mortality. The mechanisms by which the parasite invades cells are not well elucidated. We recently reported that T. cruzi up-regulates the expression of thrombospondin-1 (TSP-1) to enhance the process of cellular invasion. Here we characterize a novel TSP-1 interaction with T. cruzi that enhances cellular infection. We show that labeled TSP-1 interacts specifically with the surfac...

  9. Excellent approach to modeling urban expansion by fuzzy cellular automata: agent base model

    Science.gov (United States)

    Khajavigodellou, Yousef; Alesheikh, Ali A.; Mohammed, Abdulrazak A. S.; Chapi, Kamran

    2014-09-01

    Recently, the interaction between humans and their environment is the one of important challenges in the world. Landuse/ cover change (LUCC) is a complex process that includes actors and factors at different social and spatial levels. The complexity and dynamics of urban systems make the applicable practice of urban modeling very difficult. With the increased computational power and the greater availability of spatial data, micro-simulation such as the agent based and cellular automata simulation methods, has been developed by geographers, planners, and scholars, and it has shown great potential for representing and simulating the complexity of the dynamic processes involved in urban growth and land use change. This paper presents Fuzzy Cellular Automata in Geospatial Information System and remote Sensing to simulated and predicted urban expansion pattern. These FCA-based dynamic spatial urban models provide an improved ability to forecast and assess future urban growth and to create planning scenarios, allowing us to explore the potential impacts of simulations that correspond to urban planning and management policies. A fuzzy inference guided cellular automata approach. Semantic or linguistic knowledge on Land use change is expressed as fuzzy rules, based on which fuzzy inference is applied to determine the urban development potential for each pixel. The model integrates an ABM (agent-based model) and FCA (Fuzzy Cellular Automata) to investigate a complex decision-making process and future urban dynamic processes. Based on this model rapid development and green land protection under the influences of the behaviors and decision modes of regional authority agents, real estate developer agents, resident agents and non- resident agents and their interactions have been applied to predict the future development patterns of the Erbil metropolitan region.

  10. Interaction English Teaching Model

    Institute of Scientific and Technical Information of China (English)

    穆宇娜

    2013-01-01

      Malash—Thomas pointed out“Interaction is a process in which people and things act upon each other through their ac⁃tions.”According to different subjects, interaction can be divided into human-computer interaction, people-people interaction and learner-content interaction. According to different forms, interactions can be divided into one-one interaction, one-more interac⁃tion and more-more interaction.“Interaction Education”means that teachers are leading parts and students are the center of class. During teaching process, teachers must lead students to discover. Demands from students can encourage teachers to inspire con⁃versely.Thus it can form a close communication between teachers and students. Teaching and learning are realized in a happy and harmonious atmosphere. Successful English teaching must take new bilateral teaching as the first part, which should let the func⁃tion of the two most important elements develop fully. Teachers should grasp opportunities to guide. Teaching methods need to be flexible, and contents of teaching need to be vivid;students should be keen to think, to participate actively, and can break the tradi⁃tion to produce fresh ideas, and in that situation the capability of students can develop fully. The educational model refers to the simplified description of detailed teaching activities. Possessing dual functions of theory and practice, the educational model is the manifestation of theoretical teaching method. The combination of interaction and educational model which are mentioned above form the“interactive teaching”model. With the coming of economic globalization and integration of science and technology, now communications are increasing with each passing day. If you want to take part in or to get in touch with others, you must use lan⁃guage. English has been learnt for 10 years in Middle school and in college, but it can’t be spoken very fluently. That is a realistic picture as the result of an

  11. Photonic crystals as templates and active devices for cellular and molecular interactions

    Science.gov (United States)

    Sonek, G. J.

    2005-04-01

    Photonic crystals are emerging as an important class of engineered nanophotonic devices that possess unique optical properties and which can also provide textured surfaces for the study and control of cellular and molecular interactions. From among the many types of photonic crystal structures, two-dimensional (2D) and planar (slab) photonic crystals are the most attractive because of their ability to support guided-wave and active optical devices in semiconductor and polymer materials, serve as templates for device replication, and interface with colloidal and nanoparticle systems. This paper reports on the results of modeling and design efforts that show how 2d and slab silicon photonic crystals, based on their in-plane optical waveguiding and out-of-plane radiation properties, might be used to probe surface-bound cells and molecules or perform localized spectroscopy. The results of a parametric analysis show that photonic crystals comprised of high-index contrast materials (e.g. Si, air) are sensitive to geometric and material factors, potentially making them an effective medium to study molecular and cellular interactions critical to a number of biotechnological applications

  12. Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

    Directory of Open Access Journals (Sweden)

    Natalie Berestovsky

    Full Text Available The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them

  13. Cellular interactions of surface modified nanoporous silicon particles

    Science.gov (United States)

    Bimbo, Luis M.; Sarparanta, Mirkka; Mäkilä, Ermei; Laaksonen, Timo; Laaksonen, Päivi; Salonen, Jarno; Linder, Markus B.; Hirvonen, Jouni; Airaksinen, Anu J.; Santos, Hélder A.

    2012-05-01

    In this study, the self-assembly of hydrophobin class II (HFBII) on the surface of thermally hydrocarbonized porous silicon (THCPSi) nanoparticles was investigated. The HFBII-coating converted the hydrophobic particles into more hydrophilic ones, improved the particles' cell viability in both HT-29 and Caco-2 cell lines compared to uncoated particles, and enhanced the particles' cellular association. The amount of HFBII adsorbed onto the particles was also successfully quantified by both the BCA assay and a HPLC method. Importantly, the permeation of a poorly water-soluble drug, indomethacin, loaded into THCPSi particles across Caco-2 monolayers was not affected by the protein coating. In addition, 125I-radiolabelled HFBII did not extensively permeate the Caco-2 monolayer and was found to be stably adsorbed onto the THCPSi nanoparticles incubated in pH 7.4, which renders the particles the possibility for further track-imaging applications. The results highlight the potential of HFBII coating for improving wettability, increasing biocompatibility and possible intestinal association of PSi nanoparticulates for drug delivery applications.In this study, the self-assembly of hydrophobin class II (HFBII) on the surface of thermally hydrocarbonized porous silicon (THCPSi) nanoparticles was investigated. The HFBII-coating converted the hydrophobic particles into more hydrophilic ones, improved the particles' cell viability in both HT-29 and Caco-2 cell lines compared to uncoated particles, and enhanced the particles' cellular association. The amount of HFBII adsorbed onto the particles was also successfully quantified by both the BCA assay and a HPLC method. Importantly, the permeation of a poorly water-soluble drug, indomethacin, loaded into THCPSi particles across Caco-2 monolayers was not affected by the protein coating. In addition, 125I-radiolabelled HFBII did not extensively permeate the Caco-2 monolayer and was found to be stably adsorbed onto the THCPSi

  14. WWW Business Applications Based on the Cellular Model

    Institute of Scientific and Technical Information of China (English)

    Toshio Kodama; Tosiyasu L. Kunii; Yoichi Seki

    2008-01-01

    A cellular model based on the Incrementally Modular Abstraction Hierarchy (IMAH) is a novel model that can represent the architecture of and changes in cyberworlds, preserving invariants from a general level to a specific one. We have developed a data processing system called the Cellular Data System (CDS). In the development of business applications, you can prevent combinatorial explosion in the process of business design and testing by using CDS. In this paper, we have first designed and implemented wide-use algebra on the presentation level. Next, we have developed and verified the effectiveness of two general business applications using CDS: 1) a customer information management system, and 2) an estimate system.

  15. Lattice gas cellular automata and lattice Boltzmann models an introduction

    CERN Document Server

    Wolf-Gladrow, Dieter A

    2000-01-01

    Lattice-gas cellular automata (LGCA) and lattice Boltzmann models (LBM) are relatively new and promising methods for the numerical solution of nonlinear partial differential equations. The book provides an introduction for graduate students and researchers. Working knowledge of calculus is required and experience in PDEs and fluid dynamics is recommended. Some peculiarities of cellular automata are outlined in Chapter 2. The properties of various LGCA and special coding techniques are discussed in Chapter 3. Concepts from statistical mechanics (Chapter 4) provide the necessary theoretical background for LGCA and LBM. The properties of lattice Boltzmann models and a method for their construction are presented in Chapter 5.

  16. Modeling and Performance Analyses of Hybrid Cellular and Broadcasting Networks

    Directory of Open Access Journals (Sweden)

    Peter Unger

    2009-01-01

    Full Text Available Mobile communication services are getting more and more important and, in particular, multimedia services have attracted the interest of the users. Mobile TV is one of the most demanded candidates. Powerful and efficient communication systems are needed, which provide high capacities, especially at the downlink. Furthermore, interactivity is essential for supporting the user needs and to extend the service offering. As one possible solution to meet the mentioned requirements, we consider the combination of the cellular network UMTS and the mobile broadcast network DVB-H, which form a hybrid network. We investigate the performance of hybrid networks and develop a system model, which describes the hybrid network and the load switching between both networks. One of the contributions is the definition of the switching bound concept, which represents an efficient tool to assess the necessity and the feasibility of hybrid networks and the amount of load switching. The performance indicators cell load and grade of service are analyzed by using theoretical and realistic scenarios.

  17. Simulation of evacuation processes using a bionics-inspired cellular automaton model for pedestrian dynamics

    OpenAIRE

    Kirchner, Ansgar; Schadschneider, Andreas

    2002-01-01

    We present simulations of evacuation processes using a recently introduced cellular automaton model for pedestrian dynamics. This model applies a bionics approach to describe the interaction between the pedestrians using ideas from chemotaxis. Here we study a rather simple situation, namely the evacuation from a large room with one or two doors. It is shown that the variation of the model parameters allows to describe different types of behaviour, from regular to panic. We find a non-monotoni...

  18. PHANTOM MODEL OF HUMAN BRAIN TISSUE FOR CELLULAR PHONE FREQUENCIES IN ELECTROMAGNETIC FIELD RADIATION ABSORPTION STUDIES

    OpenAIRE

    Özen, Şükrü; Köylü, Halis

    2010-01-01

    ABSTRACTThere is a necessity of tissue equivalent (phantom) models in research of electromagnetic (EM) effects in biologic tissues. Recently, many kinds of tissue models depend on the different aim were proposed. So many studies were carried on the interaction of human-head and cellular phone. The most of them are related to numerical models. Owing to difficulty of study on human body, simulation of human tissues is required. In this study two different, for 900MHz and for 1800MHz, brain equi...

  19. Modeling evolution and immune system by cellular automata

    Energy Technology Data Exchange (ETDEWEB)

    Bezzi, M. [Scuola Internazionale Superiore di Studi Avanzati, Trieste (Italy); Istituto Nazionale di Fisica della Materia, Florence (Italy)

    2001-07-01

    In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section.

  20. Modeling evolution and immune system by cellular automata

    International Nuclear Information System (INIS)

    In this review the behavior of two different biological systems is investigated using cellular automata. Starting from this spatially extended approach it is also tried, in some cases, to reduce the complexity of the system introducing mean-field approximation, and solving (or trying to solve) these simplified systems. It is discussed the biological meaning of the results, the comparison with experimental data (if available) and the different features between spatially extended and mean-field versions. The biological systems considered in this review are the following: Darwinian evolution in simple ecosystems and immune system response. In the first section the main features of molecular evolution are introduced, giving a short survey of genetics for physicists and discussing some models for prebiotic systems and simple ecosystems. It is also introduced a cellular automaton model for studying a set of evolving individuals in a general fitness landscape, considering also the effects of co-evolution. In particular the process of species formation (speciation) is described in sect. 5. The second part deals with immune system modeling. The biological features of immune response are discussed, as well as it is introduced the concept of shape space and of idiotypic network. More detailed reviews which deal with immune system models (mainly focused on idiotypic network models) can be found. Other themes here discussed: the applications of CA to immune system modeling, two complex cellular automata for humoral and cellular immune response. Finally, it is discussed the biological data and the general conclusions are drawn in the last section

  1. Station Model for Rail Transit System Using Cellular Automata

    Institute of Scientific and Technical Information of China (English)

    XUN Jing; NING Bin; LI Ke-Ping

    2009-01-01

    In this paper, we propose a new cellular automata model to simulate the railway traffic at station.Based on NaSch model, the proposed station model is composed of the main track and the siding track.Two different schemes for trains passing through station are considered.One is the scheme of "pass by the main track, start and stop by the siding track".The other is the scheme of "two tracks play the same role".We simulate the train movement using the proposed model and analyze the traffic flow at station.The simulation results demonstrate that the proposed cellular automata model can be successfully used for the simulations of railway traffic.Some characteristic behaviors of railway traffic flow can be reproduced.Moreover, the simulation values of the minimum headway are close to the theoretical values.This result demonstrates the dependability and availability of the proposed model.

  2. Cellular worlds: a framework for modeling micro - macro dynamics

    OpenAIRE

    H Couclelis

    1985-01-01

    Cellular spaces have recently received a lot of attention in computer science and elsewhere as models capable of bridging the gap between disaggregate and aggregate description. Despite their obvious spatial interpretation, standard cell-space models are too constrained by their background conventions to be useful in realistic geographic applications. In this paper, a generalization of the cell-space principle is presented, based on discrete model theory, and then applied to a hypothetical bu...

  3. A Modified Cellular Automaton Model for Traffic Flow

    Institute of Scientific and Technical Information of China (English)

    葛红霞; 董力耘; 雷丽; 戴世强

    2004-01-01

    A modified cellular automaton model for traffic flow was proposed. A novel concept about the changeable security gap was introduced and a parameter related to the variable security gap was determined. The fundamental diagram obtained by simulation shows that the maximum flow more approaches to the observed data than that of the NaSch model, indicating that the presented model is more reasonable and realistic.

  4. Interactions between X-rays and antimitotic drugs: cellular effects

    International Nuclear Information System (INIS)

    The interactions between three drugs and X-rays were examined in rat hepatoma cells in vitro. Incubation with Daunomycine or 9-hydroxy ellipticine decreases the survival of both exponential and plateau phase cells, whereas cis-Pt (II) decreases the survival of plateau cells, especially irradiated in anoxia. The decrease in the Do was greater when the cells were incubated with the drugs prior to X-irradiation, and was greater in the case of plateau cells than in the case of exponential cells. The repair of potentially lethal damages was inhibited by these three compounds. However, the repair of sublethal damages was inhibited by cis-Pt II, but was modified neither by Daunomycine nor 9-hydroxy ellipticine

  5. Interactions of the HSV-1 UL25 Capsid Protein with Cellular Microtubule-associated Protein

    Institute of Scientific and Technical Information of China (English)

    Lei GUO; Ying ZHANG; Yan-chun CHE; Wen-juan WU; Wei-zhong LI; Li-chun WANG; Yun LIAO; Long-ding LIU; Qi-han LI

    2008-01-01

    An interaction between the HSV-1 UL25 capsid protein and cellular microtubule-associated protein was found using a yeast two-hybrid screen and β-D-galactosidase activity assays. Immunofluorescence microscopy of the UL25 protein demonstrated its co-localization with cellular microtubule-associated protein in the plasma membrane. Further investigations with deletion mutants suggest that UL25 is likely to have a function in the nucleus.

  6. Predictive modeling of multicellular structure formation by using Cellular Particle Dynamics simulations

    Science.gov (United States)

    McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

    2014-03-01

    Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  7. The brittleness model of complex system based on cellular automata

    Institute of Scientific and Technical Information of China (English)

    LIN De-ming; JIN Hong-zhang; LI Qi; WU Hong-mei

    2004-01-01

    Now the research on the complex system is a hot spot. Brittleness is one of the basic characteristics of a complex system. In a complex system, after one of subsystems is struck to be collapsed, the whole system will collapse. Meanwhile, cellular automata is a discrete dynamic system. When the rule is given, the cellular automata could be defined. Then it can imitate the complex action. Cellular automata is used to simulate the brittleness action in this study. Entropy was used to analyze the action and get the rule. Then,three normal brittleness models were given. The result shows that the brittleness of complex system is existent and in addition some important behavior mode of complex system brittleness has been achieved.

  8. Cellular automata model of magnetospheric-ionospheric coupling

    Directory of Open Access Journals (Sweden)

    B. V. Kozelov

    Full Text Available We propose a cellular automata model (CAM to describe the substorm activity of the magnetospheric-ionospheric system. The state of each cell in the model is described by two numbers that correspond to the energy content in a region of the current sheet in the magnetospheric tail and to the conductivity of the ionospheric domain that is magnetically connected with this region. The driving force of the system is supposed to be provided by the solar wind that is convected along the two boundaries of the system. The energy flux inside is ensured by the penetration of the energy from the solar wind into the array of cells (magnetospheric tail with a finite velocity. The third boundary (near to the Earth is closed and the fourth boundary is opened, thereby modeling the flux far away from the tail. The energy dissipation in the system is quite similar to other CAM models, when the energy in a particular cell exceeds some pre-defined threshold, and the part of the energy excess is redistributed between the neighbouring cells. The second number attributed to each cell mimics ionospheric conductivity that can allow for a part of the energy to be shed on field-aligned currents. The feedback between "ionosphere" and "magnetospheric tail" is provided by the change in a part of the energy, which is redistributed in the tail when the threshold is surpassed. The control parameter of the model is the z-component of the interplanetary magnetic field (Bz IMF, "frozen" into the solar wind. To study the internal dynamics of the system at the beginning, this control parameter is taken to be constant. The dynamics of the system undergoes several bifurcations, when the constant varies from - 0.6 to - 6.0. The Bz IMF input results in the periodic transients (activation regions and the inter-transient period decreases with the decrease of Bz. At the same time the onset of activations in the array shifts towards the "Earth". When the modulus of the Bz IMF exceeds some

  9. Cellular Automata Models Applied to the Study of Landslide Dynamics

    Science.gov (United States)

    Liucci, Luisa; Melelli, Laura; Suteanu, Cristian

    2015-04-01

    Landslides are caused by complex processes controlled by the interaction of numerous factors. Increasing efforts are being made to understand the spatial and temporal evolution of this phenomenon, and the use of remote sensing data is making significant contributions in improving forecast. This paper studies landslides seen as complex dynamic systems, in order to investigate their potential Self Organized Critical (SOC) behavior, and in particular, scale-invariant aspects of processes governing the spatial development of landslides and their temporal evolution, as well as the mechanisms involved in driving the system and keeping it in a critical state. For this purpose, we build Cellular Automata Models, which have been shown to be capable of reproducing the complexity of real world features using a small number of variables and simple rules, thus allowing for the reduction of the number of input parameters commonly used in the study of processes governing landslide evolution, such as those linked to the geomechanical properties of soils. This type of models has already been successfully applied in studying the dynamics of other natural hazards, such as earthquakes and forest fires. The basic structure of the model is composed of three modules: (i) An initialization module, which defines the topographic surface at time zero as a grid of square cells, each described by an altitude value; the surface is acquired from real Digital Elevation Models (DEMs). (ii) A transition function, which defines the rules used by the model to update the state of the system at each iteration. The rules use a stability criterion based on the slope angle and introduce a variable describing the weakening of the material over time, caused for example by rainfall. The weakening brings some sites of the system out of equilibrium thus causing the triggering of landslides, which propagate within the system through local interactions between neighboring cells. By using different rates of

  10. Fire Spread Model for Old Towns Based on Cellular Automaton

    Institute of Scientific and Technical Information of China (English)

    GAO Nan; WENG Wenguo; MA Wei; NI Shunjiang; HUANG Quanyi; YUAN Hongyong

    2008-01-01

    Old towns like Lijiang have enormous historic,artistic,and architectural value.The buildings in such old towns are usually made of highly combustible materials,such as wood and grass.If a fire breaks out,it will spread to multiple buildings,so fire spreading and controlling in old towns need to be studied.This paper presents a fire spread model for old towns based on cellular automaton.The cellular automaton rules were set according to historical fire data in empirical formulas.The model also considered the effects of climate.The simulation results were visualized in a geography information system.An example of a fire spread in Lijiang was investigated with the results showing that this model provides a realistic tool for predicting fire spread in old towns.Fire brigades can use this tool to predict when and how a fire spreads to minimize the losses.

  11. An intelligent floor field cellular automata model for pedestrian dynamics

    CERN Document Server

    Kirik, Ekaterina; Krouglov, Dmitriy

    2009-01-01

    A stochastic cellular automata (CA) model for pedestrian dynamics is presented. Our goal is to simulate different types of pedestrian movement, from regular to panic. But here we emphasize regular situations which imply that pedestrians analyze environment and choose their route more carefully. And transition probabilities have to depict such effect. The potentials of floor fields and environment analysis are combined in the model obtained. People patience is included in the model. This makes simulation of pedestrians movement more realistic. Some simulation results are presented and comparison with basic FF-model is made.

  12. A cellular automata model of Ebola virus dynamics

    Science.gov (United States)

    Burkhead, Emily; Hawkins, Jane

    2015-11-01

    We construct a stochastic cellular automaton (SCA) model for the spread of the Ebola virus (EBOV). We make substantial modifications to an existing SCA model used for HIV, introduced by others and studied by the authors. We give a rigorous analysis of the similarities between models due to the spread of virus and the typical immune response to it, and the differences which reflect the drastically different timing of the course of EBOV. We demonstrate output from the model and compare it with clinical data.

  13. Car Deceleration Considering Its Own Velocity in Cellular Automata Model

    Institute of Scientific and Technical Information of China (English)

    LI Ke-Ping

    2006-01-01

    In this paper, we propose a new cellular automaton model, which is based on NaSch traffic model. In our method, when a car has a larger velocity, if the gap between the car and its leading car is not enough large, it will decrease. The aim is that the following car has a buffer space to decrease its velocity at the next time, and then avoid to decelerate too high. The simulation results show that using our model, the car deceleration is realistic, and is closer to thefield measure than that of NaSch model.

  14. Simulations of Living Cell Origins Using a Cellular Automata Model

    Science.gov (United States)

    Ishida, Takeshi

    2014-04-01

    Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

  15. Mathematical model for flood routing based on cellular automaton

    Directory of Open Access Journals (Sweden)

    Xin CAI

    2014-04-01

    Full Text Available Increasing frequency and severity of flooding have caused tremendous damage in China, requiring more essential countermeasures to alleviate the damage. In this study, the dynamic simulation property of a cellular automaton was used to make further progress in flood routing. In consideration of terrain’s influence on flood routing, we regarded the terrain elevation as an auxiliary attribute of a two-dimensional cellular automaton in path selection for flood routing and developed a mathematical model based on a cellular automaton. A numerical case of propagation of an outburst flood in an area of the lower Yangtze River was analyzed with both the fixed-step and variable-step models. The results show that the flood does not spread simultaneously in all directions, but flows into the lower place first, and that the submerged area grows quickly at the beginning, but slowly later on. The final submerged areas obtained from the two different models are consistent, and the flood volume balance test shows that the flood volume meets the requirement of the total volume balance. The analysis of the case shows that the proposed model can be a valuable tool for flood routing.

  16. Modeling self-organizing traffic lights with elementary cellular automata

    CERN Document Server

    Gershenson, Carlos

    2009-01-01

    There have been several highway traffic models proposed based on cellular automata. The simplest one is elementary cellular automaton rule 184. We extend this model to city traffic with cellular automata coupled at intersections using only rules 184, 252, and 136. The simplicity of the model offers a clear understanding of the main properties of city traffic and its phase transitions. We use the proposed model to compare two methods for coordinating traffic lights: a green-wave method that tries to optimize phases according to expected flows and a self-organizing method that adapts to the current traffic conditions. The self-organizing method delivers considerable improvements over the green-wave method. For low densities, the self-organizing method promotes the formation and coordination of platoons that flow freely in four directions, i.e. with a maximum velocity and no stops. For medium densities, the method allows a constant usage of the intersections, exploiting their maximum flux capacity. For high dens...

  17. A Cellular Model for Screening Neuronal Nitric Oxide Synthase Inhibitors

    OpenAIRE

    Fang, Jianguo; Silverman, Richard B.

    2009-01-01

    Nitric oxide synthase (NOS) inhibitors are potential drug candidates because it has been well demonstrated that excessive production of NO critically contributes to a range of diseases. Most inhibitors have been screened in vitro using recombinant enzymes, leading to the discovery of a variety of potent compounds. To make inhibition studies more physiologically relevant and bridge the gap between the in vitro assay and in vivo studies, we report here a cellular model for screening NOS inhibit...

  18. Cellular-Based Statistical Model for Mobile Dispersion

    OpenAIRE

    Abdulla, Mouhamed; Shayan, Yousef R.

    2013-01-01

    While analyzing mobile systems we often approximate the actual coverage surface and assume an ideal cell shape. In a multi-cellular network, because of its tessellating nature, a hexagon is more preferred than a circular geometry. Despite this reality, perhaps due to the inherent simplicity, only a model for circular based random spreading is available. However, if used, this results an unfair terminal distribution for non-circular contours. Therefore, in this paper we specifically derived an...

  19. Optimal cellular mobility for synchronization arising from the gradual recovery of intercellular interactions

    International Nuclear Information System (INIS)

    Cell movement and intercellular signaling occur simultaneously during the development of tissues, but little is known about how movement affects signaling. Previous theoretical studies have shown that faster moving cells favor synchronization across a population of locally coupled genetic oscillators. An important assumption in these studies is that cells can immediately interact with their new neighbors after arriving at a new location. However, intercellular interactions in cellular systems may need some time to become fully established. How movement affects synchronization in this situation has not been examined. Here, we develop a coupled phase oscillator model in which we consider cell movement and the gradual recovery of intercellular coupling experienced by a cell after movement, characterized by a moving rate and a coupling recovery rate, respectively. We find (1) an optimal moving rate for synchronization and (2) a critical moving rate above which achieving synchronization is not possible. These results indicate that the extent to which movement enhances synchrony is limited by a gradual recovery of coupling. These findings suggest that the ratio of time scales of movement and signaling recovery is critical for information transfer between moving cells. (paper)

  20. Host-Parasite Interaction of Root-Knot Nematodes (Nematoda: Meloidogynidae): Cellular and Molecular Aspect

    OpenAIRE

    Gökhan Aydınlı; Sevilhan Mennan

    2014-01-01

    Root-knot nematodes (Meloidogyne spp.) have specialized and complex relationships with their host plants. A better understanding of interaction between nematode and their host will help to provide new point of view for root-knot nematode management. For this purpose, recently investigations on cellular and molecular basis of root-knot nematode parasitism and host response were reviewed.

  1. A `Clicked' Tetrameric Hydroxamic Acid Glycopeptidomimetic Antagonizes Sugar-Lectin Interactions On The Cellular Level

    Science.gov (United States)

    Zhang, Hai-Lin; Zang, Yi; Xie, Juan; Li, Jia; Chen, Guo-Rong; He, Xiao-Peng; Tian, He

    2014-07-01

    A tetrameric N-acetyl galactosaminyl (GalNAc) peptidomimetic was constructed by N-acetylation of repeating proline-based hydroxamic acid units, followed by a convergent `click chemistry' coupling. This novel glycopeptidomimetic was determined to effectively antagonize the interaction between a transmembrane hepatic lectin and GalNAc on the cellular level.

  2. JSPAM: Interacting galaxies modeller

    Science.gov (United States)

    Wallin, John F.; Holincheck, Anthony; Harvey, Allen

    2015-11-01

    JSPAM models galaxy collisions using a restricted n-body approach to speed up computation. Instead of using a softened point-mass potential, the software supports a modified version of the three component potential created by Hernquist (1994, ApJS 86, 389). Although spherically symmetric gravitationally potentials and a Gaussian model for the bulge are used to increase computational efficiency, the potential mimics that of a fully consistent n-body model of a galaxy. Dynamical friction has been implemented in the code to improve the accuracy of close approaches between galaxies. Simulations using this code using thousands of particles over the typical interaction times of a galaxy interaction take a few seconds on modern desktop workstations, making it ideal for rapidly prototyping the dynamics of colliding galaxies. Extensive testing of the code has shown that it produces nearly identical tidal features to those from hierarchical tree codes such as Gadget but using a fraction of the computational resources. This code was used in the Galaxy Zoo: Mergers project and is very well suited for automated fitting of galaxy mergers with automated pattern fitting approaches such as genetic algorithms. Java and Fortran versions of the code are available.

  3. Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions.

    Directory of Open Access Journals (Sweden)

    Thomas Wallach

    2013-03-01

    Full Text Available Essentially all biological processes depend on protein-protein interactions (PPIs. Timing of such interactions is crucial for regulatory function. Although circadian (~24-hour clocks constitute fundamental cellular timing mechanisms regulating important physiological processes, PPI dynamics on this timescale are largely unknown. Here, we identified 109 novel PPIs among circadian clock proteins via a yeast-two-hybrid approach. Among them, the interaction of protein phosphatase 1 and CLOCK/BMAL1 was found to result in BMAL1 destabilization. We constructed a dynamic circadian PPI network predicting the PPI timing using circadian expression data. Systematic circadian phenotyping (RNAi and overexpression suggests a crucial role for components involved in dynamic interactions. Systems analysis of a global dynamic network in liver revealed that interacting proteins are expressed at similar times likely to restrict regulatory interactions to specific phases. Moreover, we predict that circadian PPIs dynamically connect many important cellular processes (signal transduction, cell cycle, etc. contributing to temporal organization of cellular physiology in an unprecedented manner.

  4. Quantum chemical modelling of reactivity and selectivity of 1,2-dithiolanes towards retroviral and cellular zinc fingers

    Science.gov (United States)

    Topol, Igor A.; Nemukhin, Alexander V.; Burt, Stanley K.

    Interactions of 1,2-dithiolane species with zinc-containing sites, which mimic the zinc finger domains of retroviral and the cellular zinc finger proteins, have been investigated by quantum chemistry tools. According to the calculations, the immediate domains of zinc binding sites in the cellular and retroviral zinc fingers interact differently with such agents of the disulphide family. Thus, when approaching the model cellular-type domains, the molecules of 1,2-dithiolanes experience considerable potential barriers along the reaction path. However, these species react practically barrier-less with the model retroviral-type domains at the correlated DFT level. The results of the quantum chemical modelling provide firm support to the selectivity of 1,2-dithiolanes towards retroviral and cellular zinc fingers. This can be of great practical importance for the design of therapeutics that accomplish functional inactivation of the zinc fingers of the human immunodeficiency virus (HIV-1) retroviral type nucleocapsid protein NCp7.

  5. Modelling of detonation cellular structure in aluminium suspensions

    Science.gov (United States)

    Briand, A.; Veyssiere, B.; Khasainov, B. A.

    2010-12-01

    Heterogeneous detonations involving aluminium suspensions have been studied for many years for industrial safety policies, and for military and propulsion applications. Owing to their weak detonability and to the lack of available experimental results on the detonation cellular structure, numerical simulations provide a convenient way to improve the knowledge of such detonations. One major difficulty arising in numerical study of heterogeneous detonations involving suspensions of aluminium particles in oxidizing atmospheres is the modelling of aluminium combustion. Our previous two-step model provided results on the effect on the detonation cellular structure of particle diameter and characteristic chemical lengths. In this study, a hybrid model is incorporated in the numerical code EFAE, combining both kinetic and diffusion regimes in parallel. This more realistic model provides good agreement with the previous two-step model and confirms the correlations found between the detonation cell width, and particle diameter and characteristic lengths. Moreover, the linear dependence found between the detonation cell width and the induction length remains valid with the hybrid model.

  6. Cellular automata model of magnetospheric-ionospheric coupling

    OpenAIRE

    Kozelov, B. V.; Kozelova, T. V.

    2003-01-01

    We propose a cellular automata model (CAM) to describe the substorm activity of the magnetospheric-ionospheric system. The state of each cell in the model is described by two numbers that correspond to the energy content in a region of the current sheet in the magnetospheric tail and to the conductivity of the ionospheric domain that is magnetically connected with this region. The driving force of the system is supposed to be provided by the solar wind that is convected along the two b...

  7. A Realistic Cellular Automaton Model for Synchronized Traffic Flow

    Institute of Scientific and Technical Information of China (English)

    ZHAO Bo-Han; HU Mao-Bin; JIANG Rui; WU Qing-Song

    2009-01-01

    A cellular automaton model is proposed to consider the anticipation effect in drivers' behavior. It is shown that the anticipation effect can be one of the origins of synchronized traffic flow. With anticipation effect, the congested traffic flow simulated by the model exhibits the features of synchronized flow. The spatiotemporal patterns induced by an on-ramp are also consistent with the three-phaee traffic theory. Since the origin of synchronized flow is still controversial, our work can shed some light on the mechanism of synchronized flow.

  8. Cellular automata modelling of phase-change memories

    Institute of Scientific and Technical Information of China (English)

    Wanhua Yu; David Wright

    2008-01-01

    A novel approach to modelling phase-transition processes in phase change materials used for optical and electrical data storage applications is presented. The model is based on a cellular automaton (CA) approach to predict crystallization behaviour that is linked to thermal and electrical simulations to enable the study of the data writing and erasing processes. The CA approach is shown to be able to predict the evolution of the microstructure during the rapid heating and cooling cycles pertinent to data storage technology, and maps crystallization behaviour on the nanoscale. A simple example based on possible future nonvolatile phase-change random access solid-state memory is presented.

  9. Parallel Genetic Algorithms for calibrating Cellular Automata models: Application to lava flows

    International Nuclear Information System (INIS)

    Cellular Automata are highly nonlinear dynamical systems which are suitable far simulating natural phenomena whose behaviour may be specified in terms of local interactions. The Cellular Automata model SCIARA, developed far the simulation of lava flows, demonstrated to be able to reproduce the behaviour of Etnean events. However, in order to apply the model far the prediction of future scenarios, a thorough calibrating phase is required. This work presents the application of Genetic Algorithms, general-purpose search algorithms inspired to natural selection and genetics, far the parameters optimisation of the model SCIARA. Difficulties due to the elevated computational time suggested the adoption a Master-Slave Parallel Genetic Algorithm far the calibration of the model with respect to the 2001 Mt. Etna eruption. Results demonstrated the usefulness of the approach, both in terms of computing time and quality of performed simulations

  10. Modeling and simulation for train control system using cellular automata

    Institute of Scientific and Technical Information of China (English)

    LI; KePing; GAO; ZiYou; YANG; LiXing

    2007-01-01

    Train control system plays a key role in railway traffic. Its function is to manage and control the train movement on railway networks. In our previous works, based on the cellular automata (CA) model, we proposed several models and algorithms for simulating the train movement under different control system conditions. However, these models are only suitable for some simple traffic conditions. Some basic factors, which are important for train movement, are not considered. In this paper, we extend these models and algorithms and give a unified formula. Using the proposed method, we analyze and discuss the space-time diagram of railway traffic flow and the trajectories of the train movement. The numerical simulation and analytical results demonstrate that the unified CA model is an effective tool for simulating the train control system.

  11. Cellular automaton model considering headway-distance effect

    Science.gov (United States)

    Hu, Shou-Xin; Gao, Kun; Wang, Bing-Hong; Lu, Yu-Feng

    2008-05-01

    This paper presents a cellular automaton model for single-lane traffic flow. On the basis of the Nagel-Schreckenberg (NS) model, it further considers the effect of headway-distance between two successive cars on the randomization of the latter one. In numerical simulations, this model shows the following characteristics. (1) With a simple structure, this model succeeds in reproducing the hysteresis effect, which is absent in the NS model. (2) Compared with the slow-to-start models, this model exhibits a local fundamental diagram which is more consistent to empirical observations. (3) This model has much higher efficiency in dissolving congestions compared with the so-called NS model with velocity-dependent randomization (VDR model). (4) This model is more robust when facing traffic obstructions. It can resist much longer shock times and has much shorter relaxation times on the other hand. To summarize, compared with the existing models, this model is quite simple in structure, but has good characteristics.

  12. Structural modeling of sandwich structures with lightweight cellular cores

    Institute of Scientific and Technical Information of China (English)

    T. Liu; Z. C. Deng; T. J. Lu

    2007-01-01

    An effective single layered finite element (FE) computational model is proposed to predict the structural behavior of lightweight sandwich panels having two dimensional (2D) prismatic or three dimensional (3D) truss cores.Three different types of cellular core topology are considered: pyramidal truss core (3D), Kagome truss core (3D) and corrugated core (2D), representing three kinds of material anisotropy: orthotropic, monoclinic and general anisotropic. A homogenization technique is developed to obtain the homogenized macroscopic stiffness properties of the cellular core. In comparison with the results obtained by using detailed FE model, the single layered computational model cangive acceptable predictions for both the static and dynamic behaviors of orthotropic truss core sandwich panels. However, for non-orthotropic 3D truss cores, the predictions are not so well. For both static and dynamic behaviors of a 2D corrugated core sandwich panel, the predictions derived by the single layered computational model is generally acceptable when the size of the unit cell varies within a certain range, with the predictions for moderately strong or strong corrugated cores more accurate than those for weak cores.

  13. A Fluid Model for Performance Analysis in Cellular Networks

    Directory of Open Access Journals (Sweden)

    Coupechoux Marceau

    2010-01-01

    Full Text Available We propose a new framework to study the performance of cellular networks using a fluid model and we derive from this model analytical formulas for interference, outage probability, and spatial outage probability. The key idea of the fluid model is to consider the discrete base station (BS entities as a continuum of transmitters that are spatially distributed in the network. This model allows us to obtain simple analytical expressions to reveal main characteristics of the network. In this paper, we focus on the downlink other-cell interference factor (OCIF, which is defined for a given user as the ratio of its outer cell received power to its inner cell received power. A closed-form formula of the OCIF is provided in this paper. From this formula, we are able to obtain the global outage probability as well as the spatial outage probability, which depends on the location of a mobile station (MS initiating a new call. Our analytical results are compared to Monte Carlo simulations performed in a traditional hexagonal network. Furthermore, we demonstrate an application of the outage probability related to cell breathing and densification of cellular networks.

  14. Integrating cellular metabolism into a multiscale whole-body model.

    Directory of Open Access Journals (Sweden)

    Markus Krauss

    Full Text Available Cellular metabolism continuously processes an enormous range of external compounds into endogenous metabolites and is as such a key element in human physiology. The multifaceted physiological role of the metabolic network fulfilling the catalytic conversions can only be fully understood from a whole-body perspective where the causal interplay of the metabolic states of individual cells, the surrounding tissue and the whole organism are simultaneously considered. We here present an approach relying on dynamic flux balance analysis that allows the integration of metabolic networks at the cellular scale into standardized physiologically-based pharmacokinetic models at the whole-body level. To evaluate our approach we integrated a genome-scale network reconstruction of a human hepatocyte into the liver tissue of a physiologically-based pharmacokinetic model of a human adult. The resulting multiscale model was used to investigate hyperuricemia therapy, ammonia detoxification and paracetamol-induced toxication at a systems level. The specific models simultaneously integrate multiple layers of biological organization and offer mechanistic insights into pathology and medication. The approach presented may in future support a mechanistic understanding in diagnostics and drug development.

  15. Guided Inquiry and Consensus-Building Used to Construct Cellular Models

    Directory of Open Access Journals (Sweden)

    Joel I. Cohen

    2015-02-01

    Full Text Available Using models helps students learn from a “whole systems” perspective when studying the cell. This paper describes a model that employs guided inquiry and requires consensus building among students for its completion. The model is interactive, meaning that it expands upon a static model which, once completed, cannot be altered and additionally relates various levels of biological organization (molecular, organelle, and cellular to define cell and organelle function and interaction. Learning goals are assessed using data summed from final grades and from images of the student’s final cell model (plant, bacteria, and yeast taken from diverse seventh grade classes. Instructional figures showing consensus-building pathways and seating arrangements are discussed. Results suggest that the model leads to a high rate of participation, facilitates guided inquiry, and fosters group and individual exploration by challenging student understanding of the living cell.

  16. Robustness of a Cellular Automata Model for the HIV Infection

    CERN Document Server

    Figueirêdo, P H; Santos, R M Zorzenon dos

    2008-01-01

    An investigation was conducted to study the robustness of the results obtained from the cellular automata model which describes the spread of the HIV infection within lymphoid tissues [R. M. Zorzenon dos Santos and S. Coutinho, Phys. Rev. Lett. 87, 168102 (2001)]. The analysis focussed on the dynamic behavior of the model when defined in lattices with different symmetries and dimensionalities. The results illustrated that the three-phase dynamics of the planar models suffered minor changes in relation to lattice symmetry variations and, while differences were observed regarding dimensionality changes, qualitative behavior was preserved. A further investigation was conducted into primary infection and sensitiveness of the latency period to variations of the model's stochastic parameters over wide ranging values. The variables characterizing primary infection and the latency period exhibited power-law behavior when the stochastic parameters varied over a few orders of magnitude. The power-law exponents were app...

  17. A Cellular Automaton Model for Tumor Dormancy: Emergence of a Proliferative Switch

    CERN Document Server

    Chen, Duyu; Torquato, Salvatore

    2014-01-01

    Malignant cancers that lead to fatal outcomes for patients may remain dormant for very long periods of time. Although individual mechanisms such as cellular dormancy, angiogenic dormancy and immunosurveillance have been proposed, a comprehensive understanding of cancer dormancy and the "switch" from a dormant to a proliferative state still needs to be strengthened from both a basic and clinical point of view. Computational modeling enables one to explore a variety of scenarios for possible but realistic microscopic dormancy mechanisms and their predicted outcomes. The aim of this paper is to devise such a predictive computational model of dormancy with an emergent "switch" behavior. Specifically, we generalize a previous cellular automaton (CA) model for proliferative growth of solid tumor that now incorporates a variety of cell-level tumor-host interactions and different mechanisms for tumor dormancy, for example the effects of the immune system. Our new CA rules induce a natural "competition" between the tu...

  18. Simulation of root forms using cellular automata model

    International Nuclear Information System (INIS)

    This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled “A New Kind of Science” discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram’s investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations

  19. A hybrid parallel framework for the cellular Potts model simulations

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yi [Los Alamos National Laboratory; He, Kejing [SOUTH CHINA UNIV; Dong, Shoubin [SOUTH CHINA UNIV

    2009-01-01

    The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).

  20. Simulation of root forms using cellular automata model

    Science.gov (United States)

    Winarno, Nanang; Prima, Eka Cahya; Afifah, Ratih Mega Ayu

    2016-02-01

    This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled "A New Kind of Science" discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram's investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations.

  1. Simulation of root forms using cellular automata model

    Energy Technology Data Exchange (ETDEWEB)

    Winarno, Nanang, E-mail: nanang-winarno@upi.edu; Prima, Eka Cahya [International Program on Science Education, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229, Bandung40154 (Indonesia); Afifah, Ratih Mega Ayu [Department of Physics Education, Post Graduate School, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi no 229, Bandung40154 (Indonesia)

    2016-02-08

    This research aims to produce a simulation program for root forms using cellular automata model. Stephen Wolfram in his book entitled “A New Kind of Science” discusses the formation rules based on the statistical analysis. In accordance with Stephen Wolfram’s investigation, the research will develop a basic idea of computer program using Delphi 7 programming language. To best of our knowledge, there is no previous research developing a simulation describing root forms using the cellular automata model compared to the natural root form with the presence of stone addition as the disturbance. The result shows that (1) the simulation used four rules comparing results of the program towards the natural photographs and each rule had shown different root forms; (2) the stone disturbances prevent the root growth and the multiplication of root forms had been successfully modeled. Therefore, this research had added some stones, which have size of 120 cells placed randomly in the soil. Like in nature, stones cannot be penetrated by plant roots. The result showed that it is very likely to further develop the program of simulating root forms by 50 variations.

  2. Cellular toxicity (High-Throughput Cellular Assays for Modeling Toxicity in the Fish Reproductive System)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of this project is to adapt cellular in vitro assay systems of the rainbow trout pituitary, liver and ovary for high-throughput screening (HTS) of...

  3. Cellular automaton model of cell response to targeted radiation

    International Nuclear Information System (INIS)

    It has been shown that the response of cells to low doses of radiation is not linear and cannot be accurately extrapolated from the high dose response. To investigate possible mechanisms involved in the behaviour of cells under very low doses of radiation, a cellular automaton (CA) model was created. The diffusion and consumption of glucose in the culture dish were computed in parallel to the growth of cells. A new model for calculating survival probability was introduced; the communication between targeted and non-targeted cells was also included. Early results on the response of non-confluent cells to targeted irradiation showed the capability of the model to take account for the non-linear response in the low-dose domain

  4. Agonistic encounters and cellular angst: social interactions induce heat shock proteins in juvenile salmonid fish

    OpenAIRE

    Currie, Suzanne; LeBlanc, Sacha; Watters, M. Alexandrea; Gilmour, Kathleen M.

    2009-01-01

    Juvenile salmonid fish readily form dominance hierarchies when faced with limited resources. While these social interactions may result in profound behavioural and physiological stress, it is unknown if this social stress is evident at the level of the cellular stress response—specifically, the induction of stress or heat shock proteins (Hsps). Thus, the goal of our study was to determine if Hsps are induced during hierarchy formation in juvenile rainbow trout (Oncorhynchus mykiss). To this e...

  5. ELF (extremely-low-frequency) field interactions at the animal, tissue and cellular levels

    Energy Technology Data Exchange (ETDEWEB)

    Tenforde, T.S.

    1990-10-01

    A description is given of the fundamental physical properties of extremely-low-frequency (ELF) electromagnetic fields, and the mechanisms through which these fields interact with the human body at a macroscopic level. Biological responses to ELF fields at the tissue, cellular and molecular levels are summarized, including new evidence that ELF field exposure produces alterations in gene expression and the cytoplasmic concentrations of specific proteins.

  6. On the photonic cellular interaction and the electric activity of neurons in the human brain

    Czech Academy of Sciences Publication Activity Database

    Salari, V.; Tuszynski, J. A.; Bokkon, I.; Rahnama, M.; Cifra, Michal

    Vol. 329. Bristol: IOP, 2011 - (Cifra, M.; Pokorny, J.; Kučera, O.), 012006 ISSN 1742-6588. [9th International Frohlich's Symposium on Electrodynamic Activity of Living Cells - Including Microtubule Coherent Modes and Cancer Cell Physics. Praha (CZ), 01.07.2011-03.07.2011] Institutional support: RVO:67985882 Keywords : Electric activity * Cellular interaction * Empirical evidence Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  7. Interactions in Dark Energy Models

    OpenAIRE

    Zhang, Yi; Hui LI; Gong, Yungui; Zhu, Zong-Hong

    2011-01-01

    We perform a full dynamical analysis by considering the interactions between dark energy and radiation, and dark energy and dark matter. We find that the interaction helps alleviate the coincidence problem for the quintessence model.

  8. The evolution of early cellular systems viewed through the lens of biological interactions

    Directory of Open Access Journals (Sweden)

    Anthony M Poole

    2015-10-01

    Full Text Available The minimal cell concept represents a pragmatic approach to the question of how few genes are required to run a cell. This is a helpful way to build a parts-list, and has been more successful than attempts to deduce a minimal gene set for life by inferring the gene repertoire of the Last Universal Common Ancestor, as few genes trace back to this hypothetical ancestral state. However, the study of minimal cellular systems is the study of biological outliers where, by practical necessity, coevolutionary interactions are minimised or ignored. In this paper, we consider the biological context from which minimal genomes have been removed. For instance, some of the most reduced genomes are from endosymbionts and are the result of coevolutionary interactions with a host; few such organisms are ‘free-living’. As few, if any, biological systems exist in complete isolation, we expect that, as with modern life, early biological systems were part of an ecosystem, replete with organismal interactions. We favour refocusing discussions of the evolution of cellular systems on processes rather than gene counts. We therefore draw a distinction between a pragmatic minimal cell (an interesting engineering problem, a distributed genome (a system resulting from an evolutionary transition involving more than one cell and the looser coevolutionary interactions that are ubiquitous in ecosystems. Finally, we consider the distributed genome and coevolutionary interactions between genomic entities in the context of early evolution.

  9. Computer simulation of a cellular automata model for the immune response in a retrovirus system

    International Nuclear Information System (INIS)

    Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viral cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value Bca (Bcq). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at Bca (Bcq)

  10. Interactions between small viral RNAs of vesicular stomatitis virus and components of cellular gene expression.

    Science.gov (United States)

    Keene, J D

    1985-05-01

    Recent interest in the details of virus-host interactions has come to focus on molecular contacts between cell factors and components of viruses. These generally concern protein-protein and protein-nucleic acid interactions. In this review, protein-nucleic acid interactions involving viral transcription products and cell proteins are considered. Also examined here will be the hypothesis that such interactions have evolved because viruses have adopted cellular processes to favour their own replication and that the consequences of this co-evolution can be the disruption of the macromolecular functions of the cell, and eventual cytopathology. For its own survival in the long term, the host may evolve more refined mechanisms to evade the damage levied by the intruding virus. PMID:2856377

  11. A generalized cellular automata approach to modeling first order enzyme kinetics

    Indian Academy of Sciences (India)

    Abhishek Dutta; Saurajyoti Kar; Advait Apte; Ingmar Nopens; Denis Constales

    2015-04-01

    Biochemical processes occur through intermediate steps which are associated with the formation of reaction complexes. These enzyme-catalyzed biochemical reactions are inhibited in a number of ways such as inhibitors competing for the binding site directly, inhibitors deforming the allosteric site or inhibitors changing the structure of active substrate. Using an in silico approach, the concentration of various reaction agents can be monitored at every single time step, which are otherwise difficult to analyze experimentally. Cell-based models with discrete state variables, such as Cellular Automata (CA) provide an understanding of the organizational principles of interacting cellular systems to link the individual cell (microscopic) dynamics wit a particular collective (macroscopic) phenomenon. In this study, a CA model representing a first order enzyme kinetics with inhibitor activity is formulated. The framework of enzyme reaction rules described in this study is probabilistic. An extended von Neumann neighborhood with periodic boundary condition is implemented on a two-dimensional (2D) lattice framework. The effect of lattice-size variation is studied followed by a sensitivity analysis of the model output to the probabilistic parameters which represent various kinetic reaction constants in the enzyme kinetic model. This provides a deeper insight into the sensitivity of the CA model to these parameters. It is observed that cellular automata can capture the essential features of a discrete real system, consisting of space, time and state, structured with simple local rules without making complex implementations but resulting in complex but explainable patterns.

  12. Two-dimensional cellular automaton model for simulating structural evolution of binary alloys during solidification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Lin; ZHANG Cai-bei

    2006-01-01

    Two-dimensional cellular automaton(CA) simulations of phase transformations of binary alloys during solidification were reported. The modelling incorporates local concentration and heat changes into a nucleation or growth function, which is utilized by the automaton in a probabilistic fashion. These simulations may provide an efficient method of discovering how the physical processes involved in solidification processes dynamically progress and how they interact with each other during solidification. The simulated results show that the final morphology during solidification is related with the cooling conditions. The established model can be used to evaluate the phase transformation of binary alloys during solidification.

  13. Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework

    Science.gov (United States)

    Osborne, James M

    2015-01-01

    Colorectal cancer (CRC) is one of the major causes of death in the developed world and forms a canonical example of tumorigenesis. CRC arises from a string of mutations of individual cells in the colorectal crypt, making it particularly suited for multiscale multicellular modeling, where mutations of individual cells can be clearly represented and their effects readily tracked. In this paper, we present a multicellular model of the onset of colorectal cancer, utilizing the cellular Potts model (CPM). We use the model to investigate how, through the modification of their mechanical properties, mutant cells colonize the crypt. Moreover, we study the influence of mutations on the shape of cells in the crypt, suggesting possible cell- and tissue-level indicators for identifying early-stage cancerous crypts. Crucially, we discuss the effect that the motility parameters of the model (key factors in the behavior of the CPM) have on the distribution of cells within a homeostatic crypt, resulting in an optimal parameter regime that accurately reflects biological assumptions. In summary, the key results of this paper are 1) how to couple the CPM with processes occurring on other spatial scales, using the example of the crypt to motivate suitable motility parameters; 2) modeling mutant cells with the CPM; 3) and investigating how mutations influence the shape of cells in the crypt. PMID:26461973

  14. Computer Modeling of the Earliest Cellular Structures and Functions

    Science.gov (United States)

    Pohorille, Andrew

    2000-03-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test ourunderstanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes. We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides)organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10^6-10^8 time steps.

  15. Load-Aware Modeling and Analysis of Heterogeneous Cellular Networks

    CERN Document Server

    Dhillon, Harpreet S; Andrews, Jeffrey G

    2012-01-01

    Random spatial models are attractive for modeling heterogeneous cellular networks (HCNs) due to their realism, tractability, and scalability. A major limitation of such models to date in the context of HCNs is the neglect of network traffic and load: all base stations (BSs) have typically been assumed to always be transmitting. Small cells in particular will have a lighter load than macrocells, and so their contribution to the network interference may be significantly overstated in a fully loaded model. This paper incorporates a flexible notion of BS load by introducing a new idea of conditionally thinning the interference field. For a $K$-tier HCN where BSs across tiers differ in terms of transmit power, supported data rate, deployment density, and now load, we derive the coverage probability for a typical mobile, which connects to the strongest BS signal. Conditioned on this connection, the interfering BSs of the $i^{th}$ tier are assumed to transmit independently with probability $p_i$, which models the lo...

  16. A Computational Model of Cellular Response to Modulated Radiation Fields

    International Nuclear Information System (INIS)

    Purpose: To develop a model to describe the response of cell populations to spatially modulated radiation exposures of relevance to advanced radiotherapies. Materials and Methods: A Monte Carlo model of cellular radiation response was developed. This model incorporated damage from both direct radiation and intercellular communication including bystander signaling. The predictions of this model were compared to previously measured survival curves for a normal human fibroblast line (AGO1522) and prostate tumor cells (DU145) exposed to spatially modulated fields. Results: The model was found to be able to accurately reproduce cell survival both in populations which were directly exposed to radiation and those which were outside the primary treatment field. The model predicts that the bystander effect makes a significant contribution to cell killing even in uniformly irradiated cells. The bystander effect contribution varies strongly with dose, falling from a high of 80% at low doses to 25% and 50% at 4 Gy for AGO1522 and DU145 cells, respectively. This was verified using the inducible nitric oxide synthase inhibitor aminoguanidine to inhibit the bystander effect in cells exposed to different doses, which showed significantly larger reductions in cell killing at lower doses. Conclusions: The model presented in this work accurately reproduces cell survival following modulated radiation exposures, both in and out of the primary treatment field, by incorporating a bystander component. In addition, the model suggests that the bystander effect is responsible for a significant portion of cell killing in uniformly irradiated cells, 50% and 70% at doses of 2 Gy in AGO1522 and DU145 cells, respectively. This description is a significant departure from accepted radiobiological models and may have a significant impact on optimization of treatment planning approaches if proven to be applicable in vivo.

  17. Modelling interactions in fungi

    OpenAIRE

    Falconer, Ruth E; Bown, James L; White, Nia A.; Crawford, John W.

    2007-01-01

    Indeterminate organisms have received comparatively little attention in theoretical ecology and still there is much to be understood about the origins and consequences of community structure. The fungi comprise an entire kingdom of life and epitomize the indeterminate growth form. While interactions play a significant role in shaping the community structure of indeterminate organisms, to date most of our knowledge relating to fungi comes from observing interaction outcomes between two species...

  18. Heterogeneous cellular automata model for straight-through bicycle traffic at signalized intersection

    Science.gov (United States)

    Ren, Gang; Jiang, Hang; Chen, Jingxu; Huang, Zhengfeng; Lu, Lili

    2016-06-01

    This paper presents a cellular automata (CA) model to elucidate the straight-through movements of the heterogeneous bicycle traffic at signalized intersection. The CA model, via simulation, particularly exposits the dispersion phenomenon existing in the straight-through bicycle traffic. The nonlane-based cycling behavior and diverse bicycle properties are also incorporated in the CA model. A series of simulations are conducted to reveal the travel process, bicycles interaction and influence of the dispersion phenomenon. The simulation results show that the dispersion phenomenon significantly results in more bicycles interactions in terms of spilling maneuvers and overtaking maneuvers during the straight-through movements. Meanwhile, the dispersion phenomenon could contribute to the efficiency of the bicycle traffic, and straight-through bicycles need less time to depart the intersection under the circumstance of dispersion phenomenon. The simulation results are able to provide specific guideline for reasonably utilizing the dispersion phenomenon to improve the operational efficiency of straight-through bicycle traffic.

  19. Cellular automaton model of mass transport with chemical reactions

    International Nuclear Information System (INIS)

    The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes advection and diffusion in a simple way, and as no restriction is placed on the number of particles at a lattice site, it is also able to describe a wide variety of chemical reactions. Assuming molecular chaos and a smooth density function, we obtain the standard reaction-transport equations in the continuum limit. Simulations on one-and two-dimensional lattices show that the discrete model can be used to approximate the solutions of the continuum equations. We discuss discrepancies which arise from correlations between molecules and how these discrepancies disappear as the continuum limit is approached. Of particular interest are simulations displaying long-time behaviour which depends on long-wavelength statistical fluctuations not accounted for by the standard equations. The model is applied to the reactions a + b ↔ c and a + b → c with homogeneous and inhomogeneous initial conditions as well as to systems subject to autocatalytic reactions and displaying spontaneous formation of spatial concentration patterns. (author) 9 figs., 34 refs

  20. COMPARATIVE ANALYSIS OF CONGESTION CONTROL MODELS FOR CELLULAR WIRELESS NETWORK

    Directory of Open Access Journals (Sweden)

    Falade A. J

    2015-08-01

    Full Text Available Cellular wireless systems like GSM suffer from congestion resulting in overall system degradation and poor service delivery. When the traffic demand in a geographical area is high, the input traffic rate will exceed thecapacity of the output lines. This work focused on homogenous wireless network (the network traffic and resource dimensioning that are statistically identical such that the network performance evaluation can be reduced to a system with single cell and a single traffic type. Such system can employa queuing model to evaluate the performance metric of a cell in terms of blocking probability. Five congestion control models were compared in the work to ascertain their peculiarities, they are Erlang B, Erlang C, Engset (cleared, Engset (buffered, and Bernoulli. To analyze the system, an aggregate onedimensional Markov chain wasderived, such that it describes a call arrival process under the assumption that it is Poisson distributed. The models were simulated and their results show varying performances, however the Bernoulli model (Pb5 tends to show a situation that allows more users access to the system and the congestion level remain unaffected despite increase in the number of users and the offered traffic into the system.

  1. Plant-Herbivore Interaction: Dissection of the Cellular Pattern of Tetranychus urticae Feeding on the Host Plant

    Science.gov (United States)

    Bensoussan, Nicolas; Santamaria, M. Estrella; Zhurov, Vladimir; Diaz, Isabel; Grbić, Miodrag; Grbić, Vojislava

    2016-01-01

    The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is one of the most polyphagous herbivores feeding on cell contents of over 1100 plant species including more than 150 crops. It is being established as a model for chelicerate herbivores with tools that enable tracking of reciprocal responses in plant-spider mite interactions. However, despite their important pest status and a growing understanding of the molecular basis of interactions with plant hosts, knowledge of the way mites interface with the plant while feeding and the plant damage directly inflicted by mites is lacking. Here, utilizing histology and microscopy methods, we uncovered several key features of T. urticae feeding. By following the stylet path within the plant tissue, we determined that the stylet penetrates the leaf either in between epidermal pavement cells or through a stomatal opening, without damaging the epidermal cellular layer. Our recordings of mite feeding established that duration of the feeding event ranges from several minutes to more than half an hour, during which time mites consume a single mesophyll cell in a pattern that is common to both bean and Arabidopsis plant hosts. In addition, this study determined that leaf chlorotic spots, a common symptom of mite herbivory, do not form as an immediate consequence of mite feeding. Our results establish a cellular context for the plant-spider mite interaction that will support our understanding of the molecular mechanisms and cell signaling associated with spider mite feeding. PMID:27512397

  2. Cellular automaton model of crowd evacuation inspired by slime mould

    Science.gov (United States)

    Kalogeiton, V. S.; Papadopoulos, D. P.; Georgilas, I. P.; Sirakoulis, G. Ch.; Adamatzky, A. I.

    2015-04-01

    In all the living organisms, the self-preservation behaviour is almost universal. Even the most simple of living organisms, like slime mould, is typically under intense selective pressure to evolve a response to ensure their evolution and safety in the best possible way. On the other hand, evacuation of a place can be easily characterized as one of the most stressful situations for the individuals taking part on it. Taking inspiration from the slime mould behaviour, we are introducing a computational bio-inspired model crowd evacuation model. Cellular Automata (CA) were selected as a fully parallel advanced computation tool able to mimic the Physarum's behaviour. In particular, the proposed CA model takes into account while mimicking the Physarum foraging process, the food diffusion, the organism's growth, the creation of tubes for each organism, the selection of optimum tube for each human in correspondence to the crowd evacuation under study and finally, the movement of all humans at each time step towards near exit. To test the model's efficiency and robustness, several simulation scenarios were proposed both in virtual and real-life indoor environments (namely, the first floor of office building B of the Department of Electrical and Computer Engineering of Democritus University of Thrace). The proposed model is further evaluated in a purely quantitative way by comparing the simulation results with the corresponding ones from the bibliography taken by real data. The examined fundamental diagrams of velocity-density and flow-density are found in full agreement with many of the already published corresponding results proving the adequacy, the fitness and the resulting dynamics of the model. Finally, several real Physarum experiments were conducted in an archetype of the aforementioned real-life environment proving at last that the proposed model succeeded in reproducing sufficiently the Physarum's recorded behaviour derived from observation of the aforementioned

  3. Pseudospin Conserving Shell Model Interactions

    OpenAIRE

    Ginocchio, Joseph N.

    2010-01-01

    Pseudospin symmetry is approximately conserved in nuclei. Normally shell model interactions are written in terms of spin an orbital angular momentum operators, not in terms of pseudospin and pseudo-orbital angular momentum operators. We determine the shell model interactions which conserve pseudospin symmetry and pseudo-orbital angular momentum symmetry and write them in terms of spin and orbital angular momentum operators including the tensor interaction. We show that, although the tensor in...

  4. Emergent Behavior from A Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments

    CERN Document Server

    Jiao, Yang

    2011-01-01

    Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice. In vitro experiments have established that the invasive growth of malignant tumors is characterized by the dendritic invasive branches composed of chains of tumor cells emanating from the primary tumor mass. The preponderance of previous tumor simulations focused on non-invasive (or proliferative) growth. The formation of the invasive cell chains and their interactions with the primary tumor mass and host microenvironment are not well understood. Here, we present a novel cellular automaton (CA) model that enables one to efficiently simulate invasive tumor growth in a heterogeneous host microenvironment. By taking into account a variety of microscopic-scale tumor-host interactions, including the short-range mechanical interactions between tumor cells and tumor stroma, degradation of extracellular matrix by the invasive cells and oxygen/nutrient gradient driven cell motions, our CA mo...

  5. A novel model for studies of blood-mediated long-term responses to cellular transplants

    OpenAIRE

    Hårdstedt, Maria; Lindblom, Susanne; Hong, Jaan; Nilsson, Bo; Korsgren, Olle; Ronquist, Gunnar

    2015-01-01

    Aims Interaction between blood and bio-surfaces is important in many medical fields. With the aim of studying blood-mediated reactions to cellular transplants, we developed a whole-blood model for incubation of small volumes for up to 48 h. Methods Heparinized polyvinyl chloride tubing was cut in suitable lengths and sealed to create small bags. Multiple bags, with fresh venous blood, were incubated attached to a rotating wheel at 37°C. Physiological variables in blood were monitored: glucose...

  6. Modelling land surface - atmosphere interactions

    DEFF Research Database (Denmark)

    Rasmussen, Søren Højmark

    The study is investigates modelling of land surface – atmosphere interactions in context of fully coupled climatehydrological model. With a special focus of under what condition a fully coupled model system is needed. Regional climate model inter-comparison projects as ENSEMBLES have shown bias...

  7. Model of dynamic interactions

    OpenAIRE

    Klimchik, Alexandr; Pashkevich, Anatol; Caro, Stéphane

    2013-01-01

    In robotic-based machining, an interaction between the workpiece and technological tool causes essential deflections that significantly decrease the manufacturing accuracy. Relevant compliance errors highly depend on the manipulator configuration and essentially differ throughout the workspace. Their influence is especially important for heavy serial robots. To overcome this difficulty this report presents a new technique for compensation of the compliance errors caused by technological proce...

  8. Some properties of the floor field cellular automata evacuation model

    Science.gov (United States)

    Gwizdałła, Tomasz M.

    2015-02-01

    We study the process of evacuation of pedestrians from the room with the given arrangement of doors and obstacles by using the cellular automata technique. The technique which became quite popular is characterized by the discretization of time as well as space. For such a discretized space we use so-called floor field model which generally corresponds to the description of every cell by some monotonic function of distance between this cell and the closest exit. We study several types of effects. We start from some general features of model like the kind of a neighborhood or the factors disrupting the motion. Then we analyze the influence of asymmetry and size on the evacuation time. Finally we show characteristics concerning different arrangements of exits and include a particular approach to the proxemics effects. The scaling analyses help us to distinguish these cases which just reflect the geometry of the system and those which depend also on the simulation properties. All calculations are performed for a wide range of initial densities corresponding to different occupation rates as described by the typical crowd counting techniques.

  9. From equilibrium spin models to probabilistic cellular automata

    International Nuclear Information System (INIS)

    The general equivalence between D-dimensional probabilistic cellular automata (PCA) and (D + 1)-dimensional equilibrium spin models satisfying a disorder condition is first described in a pedagogical way and then used to analyze the phase diagrams, the critical behavior, and the universality classes of some automato. Diagrammatic representations of time-dependent correlation functions PCA are introduced. Two important classes of PCA are singled out for which these correlation functions simplify: (1) Quasi-Hamiltonian automata, which have a current-carrying steady state, and for which some correlation functions are those of a D-dimensional static model PCA satisfying the detailed balance condition appear as a particular case of these rules for which the current vanishes. (2) Linear (and more generally affine) PCA for which the diagrammatics reduces to a random walk problem closely related to (D + 1)-dimensional directed SAWs: both problems display a critical behavior with mean-field exponents in any dimension. The correlation length and effective velocity of propagation of excitations can be calculated for affine PCA, as is shown on an explicit D = 1 example. The authors conclude with some remarks on nonlinear PCA, for which the diagrammatics is related to reaction-diffusion processes, and which belong in some cases to the universality class of Reggeon field theory

  10. Calcitriol-copper interaction leads to non enzymatic, reactive oxygen species mediated DNA breakage and modulation of cellular redox scavengers in hepatocellular carcinoma.

    Science.gov (United States)

    Rizvi, Asim; Farhan, Mohd; Naseem, Imrana; Hadi, S M

    2016-09-01

    Calcitriol is the metabolically active form of Vitamin D and is known to kill cancer cells. Using the rat model of DEN induced hepatocellular carcinoma we show that there is a marked increase in cellular levels of copper in hepatocellular carcinoma and that calcitriol-copper interaction leads to reactive oxygen species mediated DNA breakage selectively in hepatocellular carcinoma cells. In vivo studies show that calcitriol selectively induces severe fluctuations in cellular enzymatic and non enzymatic scavengers of reactive oxygen species in the malignant tissue. Lipid peroxidation, a well established marker of oxidative stress, was found to increase, and substantial cellular DNA breakage was observed. We propose that calcitriol is a proxidant in the cellular milieu of hepatocellular carcinoma cells, and this copper mediated prooxidant action of calcitriol causes selective DNA breakage in malignant cells, while sparing normal (non malignant) cells. PMID:27343126

  11. Modeling chemical systems using cellular automata a textbook and laboratory manual

    CERN Document Server

    Kier, Lemont B; Cheng, Chao-Kun

    2006-01-01

    Provides a practical introduction to an exciting modeling paradigm for complex systems. This book discusses the nature of scientific inquiry using models and simulations, and describes the nature of cellular automata models. It gives descriptions of how cellular automata models can be used in the study of a variety of phenomena.

  12. Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems.

    Directory of Open Access Journals (Sweden)

    Jamie I MacPherson

    Full Text Available Human immunodeficiency virus type 1 (HIV-1 exploits a diverse array of host cell functions in order to replicate. This is mediated through a network of virus-host interactions. A variety of recent studies have catalogued this information. In particular the HIV-1, Human Protein Interaction Database (HHPID has provided a unique depth of protein interaction detail. However, as a map of HIV-1 infection, the HHPID is problematic, as it contains curation error and redundancy; in addition, it is based on a heterogeneous set of experimental methods. Based on identifying shared patterns of HIV-host interaction, we have developed a novel methodology to delimit the core set of host-cellular functions and their associated perturbation from the HHPID. Initially, using biclustering, we identify 279 significant sets of host proteins that undergo the same types of interaction. The functional cohesiveness of these protein sets was validated using a human protein-protein interaction network, gene ontology annotation and sequence similarity. Next, using a distance measure, we group host protein sets and identify 37 distinct higher-level subsystems. We further demonstrate the biological significance of these subsystems by cross-referencing with global siRNA screens that have been used to detect host factors necessary for HIV-1 replication, and investigate the seemingly small intersect between these data sets. Our results highlight significant host-cell subsystems that are perturbed during the course of HIV-1 infection. Moreover, we characterise the patterns of interaction that contribute to these perturbations. Thus, our work disentangles the complex set of HIV-1-host protein interactions in the HHPID, reconciles these with siRNA screens and provides an accessible and interpretable map of infection.

  13. Developing land use scenario dynamics model by the integration of system dynamics model and cellular automata model

    Institute of Scientific and Technical Information of China (English)

    HE; Chunyang; SHI; Peijun; CHEN; Jin; Li; Xiaobing; PAN; Ya

    2005-01-01

    Modeling land use scenario changes and its potential impacts on the structure and function of the ecosystem in the typical regions are helpful to understanding the interactive mechanism between land use system and ecological system. A Land Use Scenario Dynamics (LUSD) model by the integration of System Dynamics (SD) model and Cellular Automata (CA) model is developed with land use scenario changes in northern China in the next 20 years simulated in this paper. The basic idea of LUSD model is to simulate the land use scenario demands by using SD model at first, then allocate the land use scenario patterns at the local scale with the considerations of land use suitability, inheritance ability and neighborhood effect by using CA model to satisfy the balance between land use scenario demands and supply. The application of LUSD model in northern China suggests that the model has the ability to reflect the complex behavior of land use system at different scales to some extent and is a useful tool for assessing the potential impacts of land use system on ecological system. In addition, the simulated results also indicate that obvious land use changes will take place in the farming-pastoral zone of northern China in the next 20 years with cultivated land and urban land being the most active land use types.

  14. Relationship between cellular response models and biochemical mechanisms

    International Nuclear Information System (INIS)

    In most cellular response experiments, survival reflects the kinetics of a variety of damage and repair processes. Unfortunately, biochemical studies of molecular repair deal with mechanisms which cannot be readily correlated with these kinetic observations. The difference in these approaches sometimes leads to confusion over terms such as potentially-lethal and sublethal damage. These terms were introduced with operation definitions, derived from kinetic studies of cell survival, but some researchers have since attempted to associate them with specific biochemical mechanisms. Consequently, the terms are often used in totally different ways be different investigators. The use of carefully constructed models originating either out of assumptions based on mechanisms, or on kinetics, can be used to design experiments to eliminate some alternative kinetic schemes. In turn, some mechanisms may also be eliminated, resulting in a reduction in the number of mechanisms which must be investigated biochemically. One must take advantage of a wide range of specialized radiation procedures in order to accomplish this. Examples of the use of such specialized experimental designs, which have led to a more detailed understanding of the kinetics of both algal and mammalian cell responses, are discussed

  15. Cellular cardiac electrophysiology modeling with Chaste and CellML.

    Science.gov (United States)

    Cooper, Jonathan; Spiteri, Raymond J; Mirams, Gary R

    2014-01-01

    Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush-Larsen and Generalized Rush-Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a 'gold standard' for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior. PMID:25610400

  16. Four Dimensional (4-D BioChemInfoPhysics Models of Cardiac Cellular and Sub-Cellular Vibrations (Oscillations

    Directory of Open Access Journals (Sweden)

    Chang-Hua Zou

    2009-01-01

    Full Text Available Problem statement: Cardiovascular Diseases (CVD continued to be the leading cause of death. Failure or abnormal cardiac cellular or sub-cellular vibrations (oscillations could lead failure or abnormal heart beats that could cause CVD. Understanding the mechanisms of the vibrations (oscillations could help to prevent or to treat the diseases. Scientists have studied the mechanisms for more than 100 years. To our knowledge, the mechanisms are still unclear today. In this investigation, based on published data or results, conservation laws of the momentum as well as the energy, in views of biology, biochemistry, informatics and physics (BioChemInfoPhysics, we proposed our models of cardiac cellular and sub-cellular vibrations (oscillations of biological components, such as free ions in Biological Fluids (BF, Biological Membranes (BM, Ca++H+ (Ca++ and Na+K+ ATPases, Na+Ca++ exchangers (NCX, Ca++ carriers and myosin heads. Approach: Our models were described with 4-D (x, y, z, t or r, ?, z, t momentum transfer equations in mathematical physics. Results: The momentum transfer equations were solved with free and forced, damped, un-damped and over-damped, vibrations (oscillations. The biological components could be modeled as resonators or vibrators (oscillators, such as liquid plasmas, membranes, active springs, passive springs and active swings. Conclusion: We systematically provided new insights of automation (ignition and maintain, transportation, propagation and orientation of the cardiac cellular and sub-cellular vibrations (oscillations and resonances, with our BioChemInfoPhysics models of 4-D momentum transfer equations. Our modeling results implied: Auto-rhythmic cells (Sinoatrial Node Cells (SANC, Atrioventricular Node Cells (AVNC, Purkinje fibers, non-Auto-rhythmic ventricular myocytes and their Sarcoplasmic Reticulums (SR work as Biological Liquid Plasma Resonators (BLPR. The resonators were

  17. The mechanics of cellular compartmentalization as a model for tumor spreading

    Science.gov (United States)

    Fritsch, Anatol; Pawlizak, Steve; Zink, Mareike; Kaes, Josef A.

    2012-02-01

    Based on a recently developed surgical method of Michael H"ockel, which makes use of cellular confinement to compartments in the human body, we study the mechanics of the process of cell segregation. Compartmentalization is a fundamental process of cellular organization and occurs during embryonic development. A simple model system can demonstrate the process of compartmentalization: When two populations of suspended cells are mixed, this mixture will eventually segregate into two phases, whereas mixtures of the same cell type will not. In the 1960s, Malcolm S. Steinberg formulated the so-called differential adhesion hypothesis which explains the segregation in the model system and the process of compartmentalization by differences in surface tension and adhesiveness of the interacting cells. We are interested in to which extend the same physical principles affect tumor growth and spreading between compartments. For our studies, we use healthy and cancerous breast cell lines of different malignancy as well as primary cells from human cervix carcinoma. We apply a set of techniques to study their mechanical properties and interactions. The Optical Stretcher is used for whole cell rheology, while Cell-cell-adhesion forces are directly measured with a modified AFM. In combination with 3D segregation experiments in droplet cultures we try to clarify the role of surface tension in tumor spreading.

  18. Millimeter Wave Channel Modeling and Cellular Capacity Evaluation

    OpenAIRE

    Akdeniz, Mustafa Riza; Liu, Yuanpeng; Samimi, Mathew K.; Sun, Shu; Rangan, Sundeep; Rappaport, Theodore S.; Erkip, Elza

    2013-01-01

    With the severe spectrum shortage in conventional cellular bands, millimeter wave (mmW) frequencies between 30 and 300 GHz have been attracting growing attention as a possible candidate for next-generation micro- and picocellular wireless networks. The mmW bands offer orders of magnitude greater spectrum than current cellular allocations and enable very high-dimensional antenna arrays for further gains via beamforming and spatial multiplexing. This paper uses recent real-world measurements at...

  19. Models for Strong Interaction Physics

    Energy Technology Data Exchange (ETDEWEB)

    Ray, Rajarshi [Center for Astroparticle Physics and Space Science, Bose Institute, Block EN, Sector 5, Salt Lake City, Kolkata 700 091 (India)

    2011-07-15

    We review the developments in various models describing strong interaction physics. The models provide an intuitive way of understanding the complex phenomenon associated with strong interactions. Models also help us to delve into regions of couplings and other thermodynamic conditions of interest that are still out of reach of the first principle method - quantum chromodynamics. At the same to ascertain the merits of the models they should be contrasted to the results obtained from quantum chromodynamics at least in its region of validity, and to the available experimental data. Here we shall discuss about our progress in that direction.

  20. Problems, pitfalls, perspectives and potentials of quantitative theoretical models for cellular radiation action

    International Nuclear Information System (INIS)

    The problem of quantitative mathematical models in cellular radiation biology is discussed in a general way. It is emphasized that there are a number of stages, starting from the spatial pattern of energy deposition and ending with repair/misrepair processes which all need to be incorporated. Since different types of radiation commonly yield very similar dose-response curves a model which is only valid for one special case cannot claim general applicability. Interaction experiments with ultraviolet and ionizing radiation are discussed in this context. Also the role of different experimental systems (microorganisms versus mammalian cells) has to be taken into account. A number of current model approaches are discussed within this context, and it is shown that most of them do not satisfy the criterion of universal applicability and can therefore not claim to give a 'true' picture of biological reality. Shouldered survival curves are taken as an example to illustrate these points in a more specific way

  1. A Cellular Automata Model for the Study of Landslides

    Science.gov (United States)

    Liucci, Luisa; Suteanu, Cristian; Melelli, Laura

    2016-04-01

    Power-law scaling has been observed in the frequency distribution of landslide sizes in many regions of the world, for landslides triggered by different factors, and in both multi-temporal and post-event datasets, thus indicating the universal character of this property of landslides and suggesting that the same mechanisms drive the dynamics of mass wasting processes. The reasons for the scaling behavior of landslide sizes are widely debated, since their understanding would improve our knowledge of the spatial and temporal evolution of this phenomenon. Self-Organized Critical (SOC) dynamics and the key role of topography have been suggested as possible explanations. The scaling exponent of the landslide size-frequency distribution defines the probability of landslide magnitudes and it thus represents an important parameter for hazard assessment. Therefore, another - still unanswered - important question concerns the factors on which its value depends. This paper investigates these issues using a Cellular Automata (CA) model. The CA uses a real topographic surface acquired from a Digital Elevation Model to represent the initial state of the system, where the states of cells are defined in terms of altitude. The stability criterion is based on the slope gradient. The system is driven to instability through a temporal decrease of the stability condition of cells, which may be thought of as representing the temporal weakening of soil caused by factors like rainfall. A transition rule defines the way in which instabilities lead to discharge from unstable cells to the neighboring cells, deciding upon the landslide direction and the quantity of mass involved. Both the direction and the transferred mass depend on the local topographic features. The scaling properties of the area-frequency distributions of the resulting landslide series are investigated for several rates of weakening and for different time windows, in order to explore the response of the system to model

  2. Interacting factors and cellular localization of SR protein-specific kinase Dsk1

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Zhaohua, E-mail: ztang@jsd.claremont.edu [W.M. Keck Science Center, The Claremont Colleges, Claremont, CA 91711 (United States); Luca, Maria; Taggart-Murphy, Laura; Portillio, Jessica; Chang, Cathey; Guven, Ayse [W.M. Keck Science Center, The Claremont Colleges, Claremont, CA 91711 (United States); Lin, Ren-Jang [Department of Molecular and Cellular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010 (United States); Murray, Johanne; Carr, Antony [Genome Damage and Stability Center, University of Sussex, Falmer, BN1 9RQ (United Kingdom)

    2012-10-01

    Schizosaccharomyces pombe Dsk1 is an SR protein-specific kinase (SRPK), whose homologs have been identified in every eukaryotic organism examined. Although discovered as a mitotic regulator with protein kinase activity toward SR splicing factors, it remains largely unknown about what and how Dsk1 contributes to cell cycle and pre-mRNA splicing. In this study, we investigated the Dsk1 function by determining interacting factors and cellular localization of the kinase. Consistent with its reported functions, we found that pre-mRNA processing and cell cycle factors are prominent among the proteins co-purified with Dsk1. The identification of these factors led us to find Rsd1 as a novel Dsk1 substrate, as well as the involvement of Dsk1 in cellular distribution of poly(A){sup +} RNA. In agreement with its role in nuclear events, we also found that Dsk1 is mainly localized in the nucleus during G{sub 2} phase and at mitosis. Furthermore, we revealed the oscillation of Dsk1 protein in a cell cycle-dependent manner. This paper marks the first comprehensive analysis of in vivo Dsk1-associated proteins in fission yeast. Our results reflect the conserved role of SRPK family in eukaryotic organisms, and provide information about how Dsk1 functions in pre-mRNA processing and cell-division cycle.

  3. Interaction of alpha particles at the cellular level - Implications for the radiation weighting factor

    International Nuclear Information System (INIS)

    Since low dose effects of alpha particles are produced by cellular hits in a relatively small fraction of exposed cells, the present study focuses on alpha particle interactions in bronchial epithelial cells following exposure to inhaled radon progeny. A computer code was developed for the calculation of microdosimetric spectra, dose and hit probabilities for alpha particles emitted from uniform and non-uniform source distributions in cylindrical and Y-shaped bronchial airway geometries. Activity accumulations at the dividing spur of bronchial airway bifurcations produce hot spots of cellular hits, indicating that a small fraction of cells located at such sites may receive substantially higher doses. While presently available data on in vitro transformation frequencies suggest that the relative biological effectiveness for alpha particles ranges from about 3 to 10, the effect of inhomogeneous activity distributions of radon progeny may slightly increase the radiation weighting factor relative to a uniform distribution. Thus a radiation weighting factor of about 10 may be more realistic than the current value of 20, at least for lung cancer risk following inhalation of short-lived radon progeny. (authors)

  4. Interacting factors and cellular localization of SR protein-specific kinase Dsk1

    International Nuclear Information System (INIS)

    Schizosaccharomyces pombe Dsk1 is an SR protein-specific kinase (SRPK), whose homologs have been identified in every eukaryotic organism examined. Although discovered as a mitotic regulator with protein kinase activity toward SR splicing factors, it remains largely unknown about what and how Dsk1 contributes to cell cycle and pre-mRNA splicing. In this study, we investigated the Dsk1 function by determining interacting factors and cellular localization of the kinase. Consistent with its reported functions, we found that pre-mRNA processing and cell cycle factors are prominent among the proteins co-purified with Dsk1. The identification of these factors led us to find Rsd1 as a novel Dsk1 substrate, as well as the involvement of Dsk1 in cellular distribution of poly(A)+ RNA. In agreement with its role in nuclear events, we also found that Dsk1 is mainly localized in the nucleus during G2 phase and at mitosis. Furthermore, we revealed the oscillation of Dsk1 protein in a cell cycle-dependent manner. This paper marks the first comprehensive analysis of in vivo Dsk1-associated proteins in fission yeast. Our results reflect the conserved role of SRPK family in eukaryotic organisms, and provide information about how Dsk1 functions in pre-mRNA processing and cell-division cycle.

  5. The cellular membrane as a mediator for small molecule interaction with membrane proteins.

    Science.gov (United States)

    Mayne, Christopher G; Arcario, Mark J; Mahinthichaichan, Paween; Baylon, Javier L; Vermaas, Josh V; Navidpour, Latifeh; Wen, Po-Chao; Thangapandian, Sundarapandian; Tajkhorshid, Emad

    2016-10-01

    The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:27163493

  6. An antiviral disulfide compound blocks interaction between arenavirus Z protein and cellular promyelocytic leukemia protein

    International Nuclear Information System (INIS)

    The promyelocytic leukemia protein (PML) forms nuclear bodies (NB) that can be redistributed by virus infection. In particular, lymphocytic choriomeningitis virus (LCMV) influences disruption of PML NB through the interaction of PML with the arenaviral Z protein. In a previous report, we have shown that the disulfide compound NSC20625 has antiviral and virucidal properties against arenaviruses, inducing unfolding and oligomerization of Z without affecting cellular RING-containing proteins such as the PML. Here, we further studied the effect of the zinc-finger-reactive disulfide NSC20625 on PML-Z interaction. In HepG2 cells infected with LCMV or transiently transfected with Z protein constructs, treatment with NSC20625 restored PML distribution from a diffuse-cytoplasmic pattern to punctate, discrete NB which appeared identical to NB found in control, uninfected cells. Similar results were obtained in cells transfected with a construct expressing a Z mutant in zinc-binding site 2 of the RING domain, confirming that this Z-PML interaction requires the integrity of only one zinc-binding site. Altogether, these results show that the compound NSC20625 suppressed Z-mediated PML NB disruption and may be used as a tool for designing novel antiviral strategies against arenavirus infection.

  7. Evolution of altruism in spatial prisoner's dilemma: Intra- and inter-cellular interactions

    Science.gov (United States)

    Yokoi, Hiroki; Uehara, Takashi; Sakata, Tomoyuki; Naito, Hiromi; Morita, Satoru; Tainaka, Kei-ichi

    2014-12-01

    Iterated prisoner's dilemma game is carried out on lattice with “colony” structure. Each cell is regarded as a colony which contains plural players with an identical strategy. Both intra- and inter-cellular interactions are assumed. In the former a player plays with all other players in the same colony, while in the latter he plays with one player each from adjacent colonies. Spatial patterns among four typical strategies exhibit various dynamics and winners. Both theory and simulation reveal that All Cooperation (AC) wins, when the members of colony or the intensity of noise increases. This result explains the evolution of altruism in animal societies, even though errors easily occur in animal communications.

  8. Targeting the molecular and cellular interactions of the bone marrow niche in immunologic disease.

    Science.gov (United States)

    Brozowski, Jaime M; Billard, Matthew J; Tarrant, Teresa K

    2014-02-01

    Recent investigations have expanded our knowledge of the regulatory bone marrow (BM) niche, which is critical in maintaining and directing hematopoietic stem cell (HSC) self-renewal and differentiation. Osteoblasts, mesenchymal stem cells (MSCs), and CXCL12-abundant reticular (CAR) cells are niche components in close association with HSCs and have been more clearly defined in immune cell function and homeostasis. Importantly, cellular inhabitants of the BM niche signal through G protein-coupled surface receptors (GPCRs) for various appropriate immune functions. In this article, recent literature on BM niche inhabitants (HSCs, osteoblasts, MSCs, CAR cells) and their GPCR mechanistic interactions are reviewed for better understanding of the BM cells involved in immune development, immunologic disease, and current immune reconstitution therapies. PMID:24408534

  9. DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction

    Science.gov (United States)

    Ohta, Seiichi; Glancy, Dylan; Chan, Warren C. W.

    2016-02-01

    Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments.

  10. iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking.

    Directory of Open Access Journals (Sweden)

    Xuan Xiao

    Full Text Available Involved in many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, G-protein-coupled receptors (GPCRs are among the most frequent targets of therapeutic drugs. It is time-consuming and expensive to determine whether a drug and a GPCR are to interact with each other in a cellular network purely by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (dimensional structure of protein, unfortunately their usage is quite limited because the 3D structures for most GPCRs are still unknown. To overcome the situation, a sequence-based classifier, called "iGPCR-drug", was developed to predict the interactions between GPCRs and drugs in cellular networking. In the predictor, the drug compound is formulated by a 2D (dimensional fingerprint via a 256D vector, GPCR by the PseAAC (pseudo amino acid composition generated with the grey model theory, and the prediction engine is operated by the fuzzy K-nearest neighbour algorithm. Moreover, a user-friendly web-server for iGPCR-drug was established at http://www.jci-bioinfo.cn/iGPCR-Drug/. For the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated math equations presented in this paper just for its integrity. The overall success rate achieved by iGPCR-drug via the jackknife test was 85.5%, which is remarkably higher than the rate by the existing peer method developed in 2010 although no web server was ever established for it. It is anticipated that iGPCR-Drug may become a useful high throughput tool for both basic research and drug development, and that the approach presented here can also be extended to study other drug - target interaction networks.

  11. Biomaterial design for specific cellular interactions: Role of surface functionalization and geometric features

    Science.gov (United States)

    Kolhar, Poornima

    The areas of drug delivery and tissue engineering have experienced extraordinary growth in recent years with the application of engineering principles and their potential to support and improve the field of medicine. The tremendous progress in nanotechnology and biotechnology has lead to this explosion of research and development in biomedical applications. Biomaterials can now be engineered at a nanoscale and their specific interactions with the biological tissues can be modulated. Various design parameters are being established and researched for design of drug-delivery carriers and scaffolds to be implanted into humans. Nanoparticles made from versatile biomaterial can deliver both small-molecule drugs and various classes of bio-macromolecules, such as proteins and oligonucleotides. Similarly in the field of tissue engineering, current approaches emphasize nanoscale control of cell behavior by mimicking the natural extracellular matrix (ECM) unlike, traditional scaffolds. Drug delivery and tissue engineering are closely connected fields and both of these applications require materials with exceptional physical, chemical, biological, and biomechanical properties to provide superior therapy. In the current study the surface functionalization and the geometric features of the biomaterials has been explored. In particular, a synthetic surface for culture of human embryonic stem cells has been developed, demonstrating the importance of surface functionalization in maintaining the pluripotency of hESCs. In the second study, the geometric features of the drug delivery carriers are investigated and the polymeric nanoneedles mediated cellular permeabilization and direct cytoplasmic delivery is reported. In the third study, the combined effect of surface functionalization and geometric modification of carriers for vascular targeting is enunciated. These studies illustrate how the biomaterials can be designed to achieve various cellular behaviors and control the

  12. Computer Experiment on the Complex Behavior of a Two-Dimensional Cellular Automaton as a Phenomenological Model for an Ecosystem

    Science.gov (United States)

    Satoh, Kazuhiro

    1989-10-01

    Numerical studies are made on the complex behavior of a cellular automaton which serves as a phenomenological model for an ecosystem. The ecosystem is assumed to contain only three populations, i.e., a population of plants, of herbivores, and of carnivores. A two-dimensional region where organisms live is divided into square cells and the population density in each cell is regarded as a discrete variable. The influence of the physical environment and the interactions between organisms are reduced to a simple rule of cellular automaton evolution. It is found that the time dependent spatial distribution of organisms is, in general, very random and complex. However, under certain conditions, the self-organization of ordered patterns such as rotating spirals or concentric circles takes place. The relevance of the cellular automaton as a model for the ecosystem is discussed.

  13. Genetic Algorithm Calibration of Probabilistic Cellular Automata for Modeling Mining Permit Activity

    Science.gov (United States)

    Louis, S.J.; Raines, G.L.

    2003-01-01

    We use a genetic algorithm to calibrate a spatially and temporally resolved cellular automata to model mining activity on public land in Idaho and western Montana. The genetic algorithm searches through a space of transition rule parameters of a two dimensional cellular automata model to find rule parameters that fit observed mining activity data. Previous work by one of the authors in calibrating the cellular automaton took weeks - the genetic algorithm takes a day and produces rules leading to about the same (or better) fit to observed data. These preliminary results indicate that genetic algorithms are a viable tool in calibrating cellular automata for this application. Experience gained during the calibration of this cellular automata suggests that mineral resource information is a critical factor in the quality of the results. With automated calibration, further refinements of how the mineral-resource information is provided to the cellular automaton will probably improve our model.

  14. The similia principle: results obtained in a cellular model system.

    Science.gov (United States)

    Wiegant, Fred; Van Wijk, Roeland

    2010-01-01

    This paper describes the results of a research program focused on the beneficial effect of low dose stress conditions that were applied according to the similia principle to cells previously disturbed by more severe stress conditions. In first instance, we discuss criteria for research on the similia principle at the cellular level. Then, the homologous ('isopathic') approach is reviewed, in which the initial (high dose) stress used to disturb cellular physiology and the subsequent (low dose) stress are identical. Beneficial effects of low dose stress are described in terms of increased cellular survival capacity and at the molecular level as an increase in the synthesis of heat shock proteins (hsps). Both phenomena reflect a stimulation of the endogenous cellular self-recovery capacity. Low dose stress conditions applied in a homologous approach stimulate the synthesis of hsps and enhance survival in comparison with stressed cells that were incubated in the absence of low dose stress conditions. Thirdly, the specificity of the low dose stress condition is described where the initial (high dose) stress is different in nature from the subsequently applied (low dose) stress; the heterologous or 'heteropathic' approach. The results support the similia principle at the cellular level and add to understanding of how low dose stress conditions influence the regulatory processes underlying self-recovery. In addition, the phenomenon of 'symptom aggravation' which is also observed at the cellular level, is discussed in the context of self-recovery. Finally, the difference in efficiency between the homologous and the heterologous approach is discussed; a perspective is indicated for further research; and the relationship between studies on the similia principle and the recently introduced concept of 'postconditioning hormesis' is emphasized. PMID:20129172

  15. Models of Interacting Dark Energy

    CERN Document Server

    Zimdahl, W

    2012-01-01

    Any non-gravitational coupling between dark matter and dark energy modifies the cosmological dynamics. Interactions in the dark sector are considered to be relevant to address the coincidence problem. Moreover, in various models the observed accelerated expansion of the Universe is a pure interaction phenomenon. Here we review recent approaches in which a coupling between both dark components is crucial for the evolution of the Universe.

  16. Interactive Dimensioning of Parametric Models

    KAUST Repository

    Kelly, T.

    2015-05-01

    We propose a solution for the dimensioning of parametric and procedural models. Dimensioning has long been a staple of technical drawings, and we present the first solution for interactive dimensioning: A dimension line positioning system that adapts to the view direction, given behavioral properties. After proposing a set of design principles for interactive dimensioning, we describe our solution consisting of the following major components. First, we describe how an author can specify the desired interactive behavior of a dimension line. Second, we propose a novel algorithm to place dimension lines at interactive speeds. Third, we introduce multiple extensions, including chained dimension lines, controls for different parameter types (e.g. discrete choices, angles), and the use of dimension lines for interactive editing. Our results show the use of dimension lines in an interactive parametric modeling environment for architectural, botanical, and mechanical models. © 2015 The Author(s) Computer Graphics Forum © 2015 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.

  17. Cellular automata (CA) simulation of the interaction of vehicle flows and pedestrian crossings on urban low-grade uncontrolled roads

    Science.gov (United States)

    Chen, Qun; Wang, Yan

    2015-08-01

    This paper discusses the interaction of vehicle flows and pedestrian crossings on uncontrolled low-grade roads or branch roads without separating barriers in cities where pedestrians may cross randomly from any location on both sides of the road. The rules governing pedestrian street crossings are analyzed, and a cellular automata (CA) model to simulate the interaction of vehicle flows and pedestrian crossings is proposed. The influence of the interaction of vehicle flows and pedestrian crossings on the volume and travel time of the vehicle flow and the average wait time for pedestrians to cross is investigated through simulations. The main results of the simulation are as follows: (1) The vehicle flow volume decreases because of interruption from pedestrian crossings, but a small number of pedestrian crossings do not cause a significant delay to vehicles. (2) If there are many pedestrian crossings, slow vehicles will have little chance to accelerate, causing travel time to increase and the vehicle flow volume to decrease. (3) The average wait time for pedestrians to cross generally decreases with a decrease in vehicle flow volume and also decreases with an increase in the number of pedestrian crossings. (4) Temporal and spatial characteristics of vehicle flows and pedestrian flows and some interesting phenomena such as "crossing belt" and "vehicle belt" are found through the simulations.

  18. Computer simulation of a cellular automata model for the immune response in a retrovirus system

    Science.gov (United States)

    Pandey, R. B.

    1989-02-01

    Immune response in a retrovirus system is modeled by a network of three binary cell elements to take into account some of the main functional features of T4 cells, T8 cells, and viruses. Two different intercell interactions are introduced, one of which leads to three fixed points while the other yields bistable fixed points oscillating between a healthy state and a sick state in a mean field treatment. Evolution of these cells is studied for quenched and annealed random interactions on a simple cubic lattice with a nearest neighbor interaction using inhomogenous cellular automata. Populations of T4 cells and viral cells oscillate together with damping (with constant amplitude) for annealed (quenched) interaction on increasing the value of mixing probability B from zero to a characteristic value B ca ( B cq). For higher B, the average number of T4 cells increases while that of the viral infected cells decreases monotonically on increasing B, suggesting a phase transition at B ca ( B cq).

  19. Cellular-automata model of the dwarf shrubs populations and communities dynamics

    OpenAIRE

    A. S. Komarov; E. V. Zubkova; P. V. Frolov

    2015-01-01

    The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area...

  20. Stochastic Models of Vesicular Sorting in Cellular Organelles

    CERN Document Server

    Vagne, Quentin

    2016-01-01

    The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values leads to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggests an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organizati...

  1. Mathematical models and multiscale simulations of cellular secretion processes

    OpenAIRE

    González-Vélez, Virginia

    2011-01-01

    Exocytosis is the cellular process whereby a product such as a hormone or a neurotransmitter is released as a response to stimulation. There are a lot of exocytotic cells in mammals, and each cell type has their specific subcellular mechanisms, needed to achieve the final substance release. Therefore, unveiling the role of subcellular mechanisms in secretion processes is highly relevant to understand disease evolution and possible therapies. The efficiency of the coupling between stimulus...

  2. Reconciliation of object interaction models

    OpenAIRE

    Spanoudakis, George; Kim, Hyoseob

    2001-01-01

    This paper presents Reconciliation+, a tool-supported method which identifies overlaps between models of different object interactions expressed as UML sequence and/or collaboration diagrams, checks whether the overlapping elements of these models satisfy specific consistency rules, and guides developers in handling these inconsistencies. The method also keeps track of the decisions made and the actions taken in the process of managing inconsistencies.

  3. A Large Deformation Model for the Elastic Moduli of Two-dimensional Cellular Materials

    Institute of Scientific and Technical Information of China (English)

    HU Guoming; WAN Hui; ZHANG Youlin; BAO Wujun

    2006-01-01

    We developed a large deformation model for predicting the elastic moduli of two-dimensional cellular materials. This large deformation model was based on the large deflection of the inclined members of the cells of cellular materials. The deflection of the inclined member, the strain of the representative structure and the elastic moduli of two-dimensional cellular materials were expressed using incomplete elliptic integrals. The experimental results show that these elastic moduli are no longer constant at large deformation, but vary significantly with the strain. A comparison was made between this large deformation model and the small deformation model proposed by Gibson and Ashby.

  4. Special Issue: Redox Active Natural Products and Their Interaction with Cellular Signalling Pathways

    Directory of Open Access Journals (Sweden)

    Claus Jacob

    2014-11-01

    Full Text Available During the last decade, research into natural products has experienced a certain renaissance. The urgent need for more and more effective antibiotics in medicine, the demand for ecologically friendly plant protectants in agriculture, “natural” cosmetics and the issue of a sustainable and healthy nutrition in an ageing society have fuelled research into Nature’s treasure chest of “green gold”. Here, redox active secondary metabolites from plants, fungi, bacteria and other (micro-organisms often have been at the forefront of the most interesting developments. These agents provide powerful means to interfere with many, probably most cellular signaling pathways in humans, animals and lower organisms, and therefore can be used to protect, i.e., in form of antioxidants, and to frighten off or even kill, i.e., in form of repellants, antibiotics, fungicides and selective, often catalytic “sensor/effector” anticancer agents. Interestingly, whilst natural product research dates back many decades, in some cases even centuries, and compounds such as allicin and various flavonoids have been investigated thoroughly in the past, it has only recently become possible to investigate their precise interactions and mode(s of action inside living cells. Here, fluorescent staining and labelling on the one side, and appropriate detection, either qualitatively under the microscope or quantitatively in flow cytometers and plate readers, on the other, enable researchers to obtain the various pieces of information necessary to construct a fairly complete puzzle of how such compounds act and interact in living cells. Complemented by the more traditional activity assays and Western Blots, and increasingly joined by techniques such as proteomics, chemogenetic screening and mRNA profiling, these cell based bioanalytical techniques form a powerful platform for “intracellular diagnostics”. In the case of redox active compounds, especially of Reactive Sulfur

  5. In situ sensing and modeling of molecular events at the cellular level

    Science.gov (United States)

    Yang, Ruiguo

    We developed the Atomic Force Microscopy (AFM) based nanorobot in combination with other nanomechanical sensors for the investigation of cell signaling pathways. The AFM nanorobotics hinge on the superior spatial resolution of AFM in imaging and extends it into the measurement of biological processes and manipulation of biological matters. A multiple input single output control system was designed and implemented to solve the issues of nanomanipulation of biological materials, feedback, response frequency and nonlinearity. The AFM nanorobotic system therefore provide the human-directed position, velocity and force control with high frequency feedback, and more importantly it can feed the operator with the real-time imaging of manipulation result from the fast-imaging based local scanning. The use of the system has taken the study of cellular process at the molecular scale into a new level. The cellular response to the physiological conditions can be significantly manifested in cellular mechanics. Dynamic mechanical property has been regarded as biomarkers, sometimes even regulators of the signaling and physiological processes, thus the name mechanobiology. We sought to characterize the relationship between the structural dynamics and the molecular dynamics and the role of them in the regulation of cell behavior. We used the AFM nanorobotics to investigate the mechanical properties in real-time of cells that are stimulated by different chemical species. These reagents could result in similar ion channel responses but distinctive mechanical behaviors. We applied these measurement results to establish a model that describes the cellular stimulation and the mechanical property change, a "two-hit" model that comprises the loss of cell adhesion and the initiation of cell apoptosis. The first hit was verified by functional experiments: depletion of Calcium and nanosurgery to disrupt the cellular adhesion. The second hit was tested by a labeling of apoptotic markers that

  6. A mathematical model of amphibian skin epithelium with two types of transporting cellular units

    DEFF Research Database (Denmark)

    Larsen, Erik Hviid; Rasmussen, B E

    1985-01-01

    A computer model of ion transport across amphibian skin epithelium containing two types of cellular units, their relative number and sizes, and a paracellular pathway has been developed. The two cellular units are, a large Na+ transporting compartment representing the major epithelium from stratum...

  7. Predictive model to describe water migration in cellular solid foods during storage

    NARCIS (Netherlands)

    Voogt, J.A.; Hirte, A.; Meinders, M.B.J.

    2011-01-01

    BACKGROUND: Water migration in cellular solid foods during storage causes loss of crispness. To improve crispness retention, physical understanding of this process is needed. Mathematical models are suitable tools to gain this physical knowledge. RESULTS: Water migration in cellular solid foods invo

  8. Tools and Models for Integrating Multiple Cellular Networks

    Energy Technology Data Exchange (ETDEWEB)

    Gerstein, Mark [Yale Univ., New Haven, CT (United States). Gerstein Lab.

    2015-11-06

    In this grant, we have systematically investigated the integrated networks, which are responsible for the coordination of activity between metabolic pathways in prokaryotes. We have developed several computational tools to analyze the topology of the integrated networks consisting of metabolic, regulatory, and physical interaction networks. The tools are all open-source, and they are available to download from Github, and can be incorporated in the Knowledgebase. Here, we summarize our work as follow. Understanding the topology of the integrated networks is the first step toward understanding its dynamics and evolution. For Aim 1 of this grant, we have developed a novel algorithm to determine and measure the hierarchical structure of transcriptional regulatory networks [1]. The hierarchy captures the direction of information flow in the network. The algorithm is generally applicable to regulatory networks in prokaryotes, yeast and higher organisms. Integrated datasets are extremely beneficial in understanding the biology of a system in a compact manner due to the conflation of multiple layers of information. Therefore for Aim 2 of this grant, we have developed several tools and carried out analysis for integrating system-wide genomic information. To make use of the structural data, we have developed DynaSIN for protein-protein interactions networks with various dynamical interfaces [2]. We then examined the association between network topology with phenotypic effects such as gene essentiality. In particular, we have organized E. coli and S. cerevisiae transcriptional regulatory networks into hierarchies. We then correlated gene phenotypic effects by tinkering with different layers to elucidate which layers were more tolerant to perturbations [3]. In the context of evolution, we also developed a workflow to guide the comparison between different types of biological networks across various species using the concept of rewiring [4], and Furthermore, we have developed

  9. Preparation of oligodeoxynucleotide encapsulated cationic liposomes and release study with models of cellular membranes

    Directory of Open Access Journals (Sweden)

    Tamaddon AM.

    2007-05-01

    Full Text Available Cationic liposomes are used for cellular delivery of antisense oligodeoxynucleotide (AsODN, where release of encapsulated AsODN is mainly controlled by endocytosis and fusion mechanisms. In this investigation, it was tried to model such a release process that is difficult to evaluate in cell culture. For this purpose, an AsODN model (against protein kinase C-α was encapsulated in a DODAP-containing cationic liposome and evaluated for size, zeta-potential, encapsulation and ODN stability. Vesicular models of outer layer and total plasma membranes and early and late endosomal membranes were developed, based on lipid content and pH, using ether injection method. ODN release was determined by the fluorescence dequenching of encapsulated FITC-ODN. Zeta potential, size and ODN encapsulation efficiency of the prepared liposomes were -2.49 ± 7.15 mV, 108.4 nm and 73% respectively. ODN protection was 3-4 times more than that of conventional liposome/ODN complexation method. There was a correlation between model concentration and percent of ODN release. At 7.5 µM, the percent of released ODN was 76% for the cholesterol-free model of the late endosome and 16% for the early endosomal membrane; while the release was less than 11% for the models of plasma membrane. ODN release increased with temperature in the range of 4-37◦C for the late endosomal model, but not for others, possibly due to their high cholesterol contents or acidic pH. The interaction was fast and completed within 5 minutes and didn’t change in the range of 5-60 minutes. Our data are in agreement with published cell culture studies and reveal that cell-liposomes interaction can be modeled by lamellar membranes.

  10. Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

    Science.gov (United States)

    Bertazzoni, Umberto; Turci, Marco; Avesani, Francesca; Di Gennaro, Gianfranco; Bidoia, Carlo; Romanelli, Maria Grazia

    2011-01-01

    Human T-lymphotropic viruses type 1 (HTLV-1) and type 2 (HTLV-2) present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity. PMID:21994745

  11. Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

    Directory of Open Access Journals (Sweden)

    Maria Grazia Romanelli

    2011-05-01

    Full Text Available Human T-lymphotropic viruses type 1 (HTLV-1 and type 2 (HTLV-2 present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity.

  12. Dynamic modeling of cellular response to DNA damage based on p53 stress response networks

    Institute of Scientific and Technical Information of China (English)

    Jinpeng Qi; Yongsheng Ding; Shihuang Shao

    2009-01-01

    Under acute perturbations from the outside, cells can trigger self-defensive mechanisms to fight against genome stress. To investigate the cellular response to continuous ion radiation (IR), a dynamic model for p53 stress response networks at the cellular level is proposed. The model can successfully be used to simulate the dynamic processes of double-strand breaks (DSBs) generation and their repair, switch-like ataxia telangiectasia mutated (ATM) activation, oscillations occurring in the p53-MDM2 feedback loop, as well as toxins elimination triggered by p53 stress response networks. Especially, the model can predict the plausible outcomes of cellular response under different IR dose regimes.

  13. Fixed points in interacting dark energy models

    OpenAIRE

    Chen, Xi-ming; Gong, Yungui

    2008-01-01

    The dynamical behaviors of two interacting dark energy models are considered. In addition to the scaling attractors found in the non-interacting quintessence model with exponential potential, new accelerated scaling attractors are also found in the interacting dark energy models. The coincidence problem is reduced to the choice of parameters in the interacting dark energy models.

  14. Drug permeation and cellular interaction of amino acid-coated drug combination powders for pulmonary delivery.

    Science.gov (United States)

    Vartiainen, Ville; Bimbo, Luis M; Hirvonen, Jouni; Kauppinen, Esko I; Raula, Janne

    2016-05-17

    The effect of three amino acid coatings (l-leucine, l-valine and l-phenylalanine) on particle integrity, aerosolization properties, cellular interaction, cytocompatibility, and drug permeation properties of drug combination powder particles (beclomethasone dipropionate and salbutamol sulphate) for dry powder inhalation (DPI) was investigated. Particles with crystalline l-leucine coating resulted in intact separated particles, with crystalline l-valine coating in slightly sintered particles and with amorphous l-phenylalanine coating in strongly fused particles. The permeation of beclomethasone dipropionate across a Calu-3 differentiated cell monolayer was increased when compared with its physical mixture. Drug crystal formation was also observed on the Calu-3 cell monolayer. The l-leucine coated particles were further investigated for cytocompatibility in three human pulmonary (Calu-3, A549 and BEAS-2B) and one human macrophage (THP-1) cell lines, where they showed excellent tolerability. The l-leucine coated particles were also examined for their ability to elicit reactive oxygen species in pulmonary BEAS-2B and macrophage THP-1 cell lines. The study showed the influence of the amino acid coatings for particle formation and performance and their feasibility for combination therapy for pulmonary delivery. PMID:27034001

  15. Gelatin-Modified Bone Substitute with Bioactive Molecules Enhance Cellular Interactions and Bone Regeneration.

    Science.gov (United States)

    Teotia, Arun Kumar; Gupta, Ankur; Raina, Deepak Bushan; Lidgren, Lars; Kumar, Ashok

    2016-05-01

    In this work, we have synthesized injectable bone cement incorporated with gelatin to enhance cellular interaction. Human osteosarcoma Saos-2 cells derived bone morphogenetic proteins (BMP's) and a bisphosphonate (zoledronic acid (0.2 mM)) were also incorporated to cement. In vitro studies conducted using Saos-2 demonstrated enhanced cell proliferation on gelatin (0.2%w/v) cement. The differentiation of C2C12 mouse myoblast cells into bone forming cells showed 6-fold increase in ALP levels on gelatin cement. Polymerase chain reaction (PCR) for bone biomarkers showed osteoinductive potential of gelatin cement. We investigated efficacy for local delivery of these bioactive molecules in enhancing bone substitution qualities of bone cements by implanting in 3.5 mm critical size defect in tibial metaphysis of wistar rats. The rats were sacrificed after 12 weeks and 16 weeks post implantation. X-ray, micro-CT, histology, and histomorphometry analysis were performed to check bone healing. The cement materials slowly resorbed from the defect site leaving HAP creating porous matrix providing surface for bone formation. The materials showed high biocompatibility and initial bridging was observed in all the animals but maximum bone formation was observed in animals implanted with cement incorporated with zoledronic acid followed by cement with BMP's compared to other groups. PMID:27077816

  16. Interaction between core protein of classical swine fever virus with cellular IQGAP1 proetin appears essential for virulence in swine

    Science.gov (United States)

    Here we show that IQGAP1, a cellular protein that plays a pivotal role as a regulator of the cytoskeleton affecting cell adhesion, polarization and migration, interacts with Classical Swine Fever Virus (CSFV) Core protein. Sequence analyses identified a defined set of residues within CSFV Core prote...

  17. Modeling and Analysis of Cellular Networks using Stochastic Geometry: A Tutorial

    KAUST Repository

    ElSawy, Hesham

    2016-03-22

    This paper presents a tutorial on stochastic geometry (SG) based analysis for cellular networks. This tutorial is distinguished by its depth with respect to wireless communication details and its focus on cellular networks. The paper starts by modeling and analyzing the baseband interference in a basic cellular network model. Then, it characterizes signal-tointerference- plus-noise-ratio (SINR) and its related performance metrics. In particular, a unified approach to conduct error probability, outage probability, and rate analysis is presented. Although the main focus of the paper is on cellular networks, the presented unified approach applies for other types of wireless networks that impose interference protection around receivers. The paper then extends the baseline unified approach to capture cellular network characteristics (e.g., frequency reuse, multiple antenna, power control, etc.). It also presents numerical examples associated with demonstrations and discussions. Finally, we point out future research directions.

  18. Models of dyadic social interaction.

    OpenAIRE

    Griffin, Dale; Gonzalez, Richard

    2003-01-01

    We discuss the logic of research designs for dyadic interaction and present statistical models with parameters that are tied to psychologically relevant constructs. Building on Karl Pearson's classic nineteenth-century statistical analysis of within-organism similarity, we describe several approaches to indexing dyadic interdependence and provide graphical methods for visualizing dyadic data. We also describe several statistical and conceptual solutions to the 'levels of analytic' problem in ...

  19. Interacting Induced Dark Energy Model

    CERN Document Server

    Bahrehbakhsh, Amir F

    2016-01-01

    Similar to the idea of the brane world scenarios, but based on the approach of the induced matter theory, for a non--vacuum five--dimensional version of general relativity, we propose a model in which the conventional matter sources considered as all kind of the matter (the baryonic and dark) and the induced terms emerging from the extra dimension supposed to be as dark energy. Then we investigate the FLRW type cosmological equations and illustrate that the model is capable to explain respectively the deceleration and then acceleration eras of the universe expansion with an interacting term between the matter and dark energy.

  20. Effects of Mechanical Properties on Tumor Invasion: Insights from a Cellular Model

    KAUST Repository

    Li, YZ

    2014-08-01

    Understanding the regulating mechanism of tumor invasion is of crucial importance for both fundamental cancer research and clinical applications. Previous in vivo experiments have shown that invasive cancer cells dissociate from the primary tumor and invade into the stroma, forming an irregular invasive morphology. Although cell movements involved in tumor invasion are ultimately driven by mechanical forces of cell-cell interactions and tumor-host interactions, how these mechanical properties affect tumor invasion is still poorly understood. In this study, we use a recently developed two-dimensional cellular model to study the effects of mechanical properties on tumor invasion. We study the effects of cell-cell adhesions as well as the degree of degradation and stiffness of extracellular matrix (ECM). Our simulation results show that cell-cell adhesion relationship must be satisfied for tumor invasion. Increased adhesion to ECM and decreased adhesion among tumor cells result in invasive tumor behaviors. When this invasive behavior occurs, ECM plays an important role for both tumor morphology and the shape of invasive cancer cells. Increased stiffness and stronger degree of degradation of ECM promote tumor invasion, generating more aggressive tumor invasive morphologies. It can also generate irregular shape of invasive cancer cells, protruding towards ECM. The capability of our model suggests it a useful tool to study tumor invasion and might be used to propose optimal treatment in clinical applications.

  1. Cellular Automation Model of Traffic Flow Based on the Car-Following Model

    Institute of Scientific and Technical Information of China (English)

    LI Ke-Ping; GAO Zi-You

    2004-01-01

    @@ We propose a new cellular automation (CA) traffic model that is based on the car-following model. A class of driving strategies is used in the car-following model instead of the acceleration in the NaSch traffic model. In our model, some realistic driver behaviour and detailed vehicle characteristics have been taken into account, such as distance-headway and safe distance, etc. The simulation results show that our model can exhibit some traffic flow states that have been observed in the real traffic, and both of the maximum flux and the critical density are very close to the real measurement. Moreover, it is easy to extend our method to multi-lane traffic.

  2. Cellular polarization: Interaction between extrinsic bounded noises and the wave-pinning mechanism

    Science.gov (United States)

    de Franciscis, Sebastiano; d'Onofrio, Alberto

    2013-09-01

    Cell polarization (cued or uncued) is a fundamental mechanism in cell biology. As an alternative to the classical Turing bifurcation, it has been proposed that the onset of cell polarity might arise by means of the well-known phenomenon of wave-pinning [Gamba , Proc. Natl. Acad. Sci. USAPNASA60027-842410.1073/pnas.0503974102 102, 16927 (2005)]. A particularly simple and elegant deterministic model of cell polarization based on the wave-pinning mechanism has been proposed by Edelstein-Keshet and coworkers [Biophys. J.BIOJAU0006-349510.1529/biophysj.107.120824 94, 3684 (2008)]. This model consists of a small biomolecular network where an active membrane-bound factor interconverts into its inactive form that freely diffuses in the cell cytosol. However, biomolecular networks do communicate with other networks as well as with the external world. Thus, their dynamics must be considered as perturbed by extrinsic noises. These noises may have both a spatial and a temporal correlation, and in any case they must be bounded to preserve the biological meaningfulness of the perturbed parameters. Here we numerically show that the inclusion of external spatiotemporal bounded parametric perturbations in the above wave-pinning-based model of cellular polarization may sometimes destroy the polarized state. The polarization loss depends on both the extent of temporal and spatial correlations and on the kind of noise employed. For example, an increase of the spatial correlation of the noise induces an increase of the probability of cell polarization. However, if the noise is spatially homogeneous then the polarization is lost in the majority of cases. These phenomena are independent of the type of noise. Conversely, an increase of the temporal autocorrelation of the noise induces an effect that depends on the model of noise.

  3. Linking Cellular and Mechanical Processes in Articular Cartilage Lesion Formation: A Mathematical Model

    OpenAIRE

    Kapitanov, Georgi I.; Wang, Xiayi; Ayati, Bruce P; Brouillette, Marc J.; Martin, James A.

    2016-01-01

    A severe application of stress on articular cartilage can initiate a cascade of biochemical reactions that can lead to the development of osteoarthritis. We constructed a multiscale mathematical model of the process with three components: cellular, chemical, and mechanical. The cellular component describes the different chondrocyte states according to the chemicals these cells release. The chemical component models the change in concentrations of those chemicals. The mechanical component cont...

  4. Graphene nanoplatelets spontaneously translocate into the cytosol and physically interact with cellular organelles in the fish cell line PLHC-1

    Energy Technology Data Exchange (ETDEWEB)

    Lammel, Tobias; Navas, José M., E-mail: jmnavas@inia.es

    2014-05-01

    Highlights: • We assessed the cytotoxicity and uptake of graphene nanomaterials in PLHC-1 cells. • GO and CXYG nanoplatelets caused physical injury of the plasma membrane. • GO and CXYG accumulated in the cytosol and interacted with cellular organelles. • PLHC-1 cells exposed to GO/CXYG demonstrated high ROS levels but low cytotoxicity. • ROS formation was related with GO/CXYG-induced structural damage of mitochondria. - Abstract: Graphene and graphene derivatives constitute a novel class of carbon-based nanomaterials being increasingly produced and used in technical and consumer applications. Release of graphene nanoplatelets during the life cycle of these applications may result in human and environmental exposure calling for assessment of their potential to cause harm to humans and wildlife. This study aimed to assess the toxicity of graphene oxide (GO) and carboxyl graphene (CXYG) nanoplatelets to non-mammalian species using the fish cell line PLHC-1 as in vitro model. The cytotoxicity of GO and CXYG was assessed using different assays measuring alterations in plasma membrane integrity, metabolic activity, and lysosomal and mitochondrial function. The induction of oxidative stress was assessed by measuring intracellular reactive oxygen species (ROS) levels. Interaction with the plasma membrane and internalization of nanoplatelets were investigated by electron microscopy. Graphene nanoplatelets spontaneously penetrated through the plasma membrane and accumulated in the cytosol, where they further interacted with mitochondrial and nuclear membranes. PLHC-1 cells demonstrated significantly reduced mitochondrial membrane potential (MMP) and increased ROS levels at 16 μg/ml GO and CXYG (72 h), but barely any decrease in cell viability. The observation of intracellular graphene accumulations not enclosed by membranes suggests that GO and CXYG internalization in fish hepatoma cells occurs through an endocytosis-independent mechanism.

  5. Intra-cellular transport by single-headed kinesin KIF1A: effects of single-motor mechano-chemistry and steric interactions

    CERN Document Server

    Greulich, P; Garai, A; Nishinari, K; Schadschneider, A; Chowdhury, Debashish; Garai, Ashok; Greulich, Philip; Nishinari, Katsuhiro; Schadschneider, Andreas

    2006-01-01

    In eukaryotic cells, many motor proteins can move simultaneously on a single microtubule track. This leads to interesting collective phenomena like jamming. Recently we reported ({\\it Phys. Rev. Lett. {\\bf 95}, 118101 (2005)}) a lattice-gas model which describes traffic of unconventional (single-headed) kinesins KIF1A. Here we generalize this model, introducing a novel interaction parameter $c$, to account for an interesting mechano-chemical process which has not been considered in any earlier model. We have been able to extract all the parameters of the model, except $c$, from experimentally measured quantities. In contrast to earlier models of intra-cellular molecular motor traffic, our model assigns distinct ``chemical'' (or, conformational) states to each kinesin to account for the hydrolysis of ATP, the chemical fuel of the motor. Our model makes experimentally testable theoretical predictions. We determine the phase diagram of the model in planes spanned by experimentally controllable parameters, namely...

  6. Simulation Modeling by Classification of Problems: A Case of Cellular Manufacturing

    Science.gov (United States)

    Afiqah, K. N.; Mahayuddin, Z. R.

    2016-02-01

    Cellular manufacturing provides good solution approach to manufacturing area by applying Group Technology concept. The evolution of cellular manufacturing can enhance performance of the cell and to increase the quality of the product manufactured but it triggers other problem. Generally, this paper highlights factors and problems which emerge commonly in cellular manufacturing. The aim of the research is to develop a thorough understanding of common problems in cellular manufacturing. A part from that, in order to find a solution to the problems exist using simulation technique, this classification framework is very useful to be adapted during model building. Biology evolution tool was used in the research in order to classify the problems emerge. The result reveals 22 problems and 25 factors using cladistic technique. In this research, the expected result is the cladogram established based on the problems in cellular manufacturing gathered.

  7. Cellular cardiac electrophysiology modeling with Chaste and CellML

    OpenAIRE

    Cooper, Jonathan; Spiteri, Raymond J.; Mirams, Gary R

    2014-01-01

    Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model...

  8. Modelling lava flows by Cellular Nonlinear Networks (CNN: preliminary results

    Directory of Open Access Journals (Sweden)

    C. Del Negro

    2005-01-01

    Full Text Available The forecasting of lava flow paths is a complex problem in which temperature, rheology and flux-rate all vary with space and time. The problem is more difficult to solve when lava runs down a real topography, considering that the relations between characteristic parameters of flow are typically nonlinear. An alternative approach to this problem that does not use standard differential equation methods is Cellular Nonlinear Networks (CNNs. The CNN paradigm is a natural and flexible framework for describing locally interconnected, simple, dynamic systems that have a lattice-like structure. They consist of arrays of essentially simple, nonlinearly coupled dynamic circuits containing linear and non-linear elements able to process large amounts of information in real time. Two different approaches have been implemented in simulating some lava flows. Firstly, a typical technique of the CNNs to analyze spatio-temporal phenomena (as Autowaves in 2-D and in 3-D has been utilized. Secondly, the CNNs have been used as solvers of partial differential equations of the Navier-Stokes treatment of Newtonian flow.

  9. Modified cellular automaton model for modeling of microstructure and microsegregation in solidification of ternary alloys

    Institute of Scientific and Technical Information of China (English)

    ZHU Ming-fang; CAO Wei-sheng; CHEN Shuang-lin; XIE Fan-you; HONG Chunpyo; CHANG Y. Austin

    2006-01-01

    A modified cellular automaton (MCA) model has been extended to the ternary alloy system by coupling thermodynamic and phase equilibrium calculation engine PanEngine. In the present model the dendrite growth is driven by the difference between the local equilibrium liquidus temperature and local actual temperature, incorporating the effect of curvature. The local equilibrium liquidus temperature is calculated with PanEngine according to the local liquid concentrations of two solutes, which are determined by numerically solving the species transport equation in the domain. Model validation was carried out through the comparison of the simulated values to the prediction of the Scheil model for solute profiles in the primary dendrites. The simulated data with zero solid diffusivity and limited liquid diffusivity were increasingly close to the Scheil profiles as the solidification rate decreased. The simulated microstructure and microsegregation in an Al-Cu-Mg ternary alloy were compared with those obtained experimentally.

  10. Jeans type instability for a chemotactic model of cellular aggregation

    CERN Document Server

    Chavanis, Pierre-Henri

    2008-01-01

    We consider an inertial model of chemotactic aggregation generalizing the Keller-Segel model and we study the linear dynamical stability of an infinite and homogeneous distribution of cells (bacteria, amoebae, endothelial cells,...) when inertial effects are accounted for. These inertial terms model cells directional persistance. We determine the condition of instability and the growth rate of the perturbation as a function of the cell density and the wavelength of the perturbation. We discuss the differences between overdamped (Keller-Segel) and inertial models. Finally, we show the analogy between the instability criterion for biological populations and the Jeans instability criterion in astrophysics.

  11. Simulating debris flows through a hexagonal cellular automata model: SCIDDICA S3–hex

    Directory of Open Access Journals (Sweden)

    D. D’Ambrosio

    2003-01-01

    Full Text Available Cellular Automata (CA represent a formal frame for dynamical systems, which evolve on the base of local interactions. Some types of landslide, such as debris flows, match well this requirement. The latest hexagonal release (S3–hex of the deterministic model SCIDDICA, specifically developed for simulating debris flows, is described. For CA simulation purposes, landslides can be viewed as a dynamical system, subdivided into elementary parts, whose state evolves exclusively as a consequence of local interactions within a spatial and temporal discretum. Space is the world of the CA, here constituted by hexagonal cells. The attributes of each cell ("substates" describe physical characteristics. For computational reasons, the natural phenomenon is "decomposed" into a number of elementary processes, whose proper composition makes up the "transition function" of the CA. By simultaneously applying this function to all the cells, the evolution of the phenomenon can be simulated in terms of modifications of the substates. SCIDDICA S3–hex exhibits a great flexibility in modelling debris flows. With respect to the previous releases of the model, the mechanism of progressive erosion of the soil cover has been added to the transition function. Considered substates are: altitude; thickness and energy of landslide debris; depth of erodable soil cover; debris outflows. Considered elementary processes are: mobilisation triggering and effect (T1, debris outflows (I1, update of landslide debris thickness and energy (I2, and energy loss (T2.  Simulations of real debris flows, occurred in Campania (Southern Italy in May 1998 (Sarno and December 1999 (San Martino V.C. and Cervinara, have been performed for model calibration purposes; some examples of analysis are briefly described. Possible applications of the method are: risk mapping, also based on a statistical approach; evaluating the effects of mitigation actions (e.g. stream deviations, topographic

  12. A mathematical model of cortical bone remodeling at cellular level under mechanical stimulus

    Institute of Scientific and Technical Information of China (English)

    Qing-Hua Qin; Ya-Nan Wang

    2012-01-01

    A bone cell population dynamics model for cortical bone remodeling under mechanical stimulus is developed in this paper.The external experiments extracted from the literature which have not been used in the creation of the model are used to test the validity of the model.Not only can the model compare reasonably well with these experimental results such as the increase percentage of final values of bone mineral content (BMC) and bone fracture energy (BFE) among different loading schemes (which proves the validity of the model),but also predict the realtime development pattern of BMC and BFE,as well as the dynamics of osteoblasts (OBA),osteoclasts (OCA),nitric oxide (NO) and prostaglandin E2 (PGE2) for each loading scheme,which can hardly be monitored through experiment.In conclusion,the model is the first of its kind that is able to provide an insight into the quantitative mechanism of bone remodeling at cellular level by which bone cells are activated by mechanical stimulus in order to start resorption/formation of bone mass.More importantly,this model has laid a solid foundation based on which future work such as systemic control theory analysis of bone remodeling under mechanical stimulus can be investigated.The to-be identified control mechanism will help to develop effective drugs and combined nonpharmacological therapies to combat bone loss pathologies.Also this deeper understanding of how mechanical forces quantitatively interact with skeletal tissue is essential for the generation of bone tissue for tissue replacement purposes in tissue engineering.

  13. A study of a main-road cellular automata traffic flow model

    Institute of Scientific and Technical Information of China (English)

    黄乒花; 孔令江; 刘慕仁

    2002-01-01

    A main-road cellular automata traffic flow model on two dimensions is presented based on the Biham-Middleton-Levine traffic model. Its evolution equations are given and the self-organization and organization cooperation phenomenain this model are also studied by using computer simulation.

  14. Propagation Path Loss Models for 5G Urban Micro- and Macro-Cellular Scenarios

    DEFF Research Database (Denmark)

    Sun, Shu; Rappaport, Theodore S.; Rangan, Sundeep;

    2016-01-01

    This paper presents and compares two candidate large-scale propagation path loss models, the alpha-beta-gamma (ABG) model and the close-in (CI) free space reference distance model, for the design of fifth generation (5G) wireless communication systems in urban micro- and macro-cellular scenarios...

  15. Integration of logistic regression, Markov chain and cellular automata models to simulate urban expansion

    NARCIS (Netherlands)

    Jokar Arsanjani, J.; Helbich, M.; Kainz, W.; Boloorani, A.

    2013-01-01

    This research analyses the suburban expansion in the metropolitan area of Tehran, Iran. A hybrid model consisting of logistic regression model, Markov chain (MC), and cellular automata (CA) was designed to improve the performance of the standard logistic regression model. Environmental and socio-eco

  16. From molecular interaction to acute promyelocytic leukemia: Calculating leukemogenesis and remission from endogenous molecular-cellular network.

    Science.gov (United States)

    Yuan, Ruoshi; Zhu, Xiaomei; Radich, Jerald P; Ao, Ping

    2016-01-01

    Acute promyelocytic leukemia (APL) remains the best example of a malignancy that can be cured clinically by differentiation therapy. We demonstrate that APL may emerge from a dynamical endogenous molecular-cellular network obtained from normal, non-cancerous molecular interactions such as signal transduction and translational regulation under physiological conditions. This unifying framework, which reproduces APL, normal progenitor, and differentiated granulocytic phenotypes as different robust states from the network dynamics, has the advantage to study transition between these states, i.e. critical drivers for leukemogenesis and targets for differentiation. The simulation results quantitatively reproduce microarray profiles of NB4 and HL60 cell lines in response to treatment and normal neutrophil differentiation, and lead to new findings such as biomarkers for APL and additional molecular targets for arsenic trioxide therapy. The modeling shows APL and normal states mutually suppress each other, both in "wiring" and in dynamical cooperation. Leukemogenesis and recovery under treatment may be a consequence of spontaneous or induced transitions between robust states, through "passes" or "dragging" by drug effects. Our approach rationalizes leukemic complexity and constructs a platform towards extending differentiation therapy by performing "dry" molecular biology experiments. PMID:27098097

  17. On Modeling Coverage and Rate of Random Cellular Networks under Generic Channel Fading

    OpenAIRE

    Al-Hourani, Akram; Kandeepan, Sithamparanathan

    2016-01-01

    In this paper we provide an analytic framework for computing the expected downlink coverage probability, and the associated data rate of cellular networks, where base stations are distributed in a random manner. The provided expressions are in computable integral forms that accommodate generic channel fading conditions. We develop these expressions by modelling the cellular interference using stochastic geometry analysis, then we employ them for comparing the coverage resulting from various c...

  18. A cellular network model with Ginibre configured base stations

    OpenAIRE

    Miyoshi, Naoto; Shirai, Tomoyuki

    2014-01-01

    Stochastic geometry models for wireless communication networks have recently attracted much attention. This is because the performance of such networks critically depends on the spatial configuration of wireless nodes and the irregularity of the node configuration in a real network can be captured by a spatial point process. However, most analysis of such stochastic geometry models for wireless networks assumes, owing to its tractability, that the wireless nodes are deployed...

  19. Detection of regulatory circuits by integrating the cellular networks of protein–protein interactions and transcription regulation

    OpenAIRE

    Yeger-Lotem, Esti; Margalit, Hanah

    2003-01-01

    The post-genomic era is marked by huge amounts of data generated by large-scale functional genomic and proteomic experiments. A major challenge is to integrate the various types of genome-scale information in order to reveal the intra- and inter- relationships between genes and proteins that constitute a living cell. Here we present a novel application of classical graph algorithms to integrate the cellular networks of protein–protein interactions and transcription regulation. We demonstrate ...

  20. A cellular automata model for simulating fed-batch penicillin fermentation process

    Institute of Scientific and Technical Information of China (English)

    Yu Naigong; Ruan Xiaogang

    2006-01-01

    A cellular automata model to simulate penicillin fed-batch fermentation process(CAPFM)was established in this study,based on a morphologically structured dynamic penicillin production model,that is in turn based on the growth mechanism of penicillin producing microorganisms and the characteristics of penicillin fed-batch fermentation.CAPFM uses the three-dimensional cellular automata as a growth space,and a Moore-type neighborhood as the cellular neighborhood.The transition roles of CAPFM are designed based on mechanical and structural kinetic models of penicillin batch-fed fermentation processes.Every cell of CAPFM represents a single or specific number of penicillin producing microorganisms,and has various state.The simulation experimental results show that CAPFM replicates the evolutionary behavior of penicillin batch-fed fermentation processes described by the structured penicillin production kinetic model accordingly.

  1. Mathematical Modeling Predicts How Proteins Affect Cellular Communication

    OpenAIRE

    Lee Ethan; Salic Adrian; Krüger Roland; Heinrich Reinhart; Kirschner Marc W

    2003-01-01

    Wnt signaling plays an important role in both oncogenesis and development. Activation of the Wnt pathway results in stabilization of the transcriptional coactivator beta-catenin. Recent studies have demonstrated that axin, which coordinates beta-catenin degradation, is itself degraded. Although the key molecules required for transducing a Wnt signal have been identified, a quantitative understanding of this pathway has been lacking. We have developed a mathematical model for the canonical Wnt...

  2. Cellular automata cell structure for modeling heterogeneous traffic

    OpenAIRE

    Pal, Dibyendu; C.Mallikarjuna

    2010-01-01

    Gap maintaining behavior significantly affects the traffic flow modeling under heterogeneous traffic conditions. The clearance between two adjacent moving vehicles varies depending on several traffic conditions. From the data collected on the gap maintaining behavior it has been observed that vehicles maintain different gaps when travelling under different traffic conditions and this is also influenced by lateral position of the vehicle. Mallikarjuna (2007) has found that this variable gap ma...

  3. Cellular models and therapies for age-related macular degeneration

    Directory of Open Access Journals (Sweden)

    David L. Forest

    2015-05-01

    Full Text Available Age-related macular degeneration (AMD is a complex neurodegenerative visual disorder that causes profound physical and psychosocial effects. Visual impairment in AMD is caused by the loss of retinal pigmented epithelium (RPE cells and the light-sensitive photoreceptor cells that they support. There is currently no effective treatment for the most common form of this disease (dry AMD. A new approach to treating AMD involves the transplantation of RPE cells derived from either human embryonic or induced pluripotent stem cells. Multiple clinical trials are being initiated using a variety of cell therapies. Although many animal models are available for AMD research, most do not recapitulate all aspects of the disease, hampering progress. However, the use of cultured RPE cells in AMD research is well established and, indeed, some of the more recently described RPE-based models show promise for investigating the molecular mechanisms of AMD and for screening drug candidates. Here, we discuss innovative cell-culture models of AMD and emerging stem-cell-based therapies for the treatment of this vision-robbing disease.

  4. Equal Distribution Model of Epidemic Drugs Based on a Cellular Automata Model

    Directory of Open Access Journals (Sweden)

    Huang Xinyi

    2015-01-01

    Full Text Available The epidemic spreading of infectious disease is a process of evolution over time. Based on the cellular automata model[1], this paper analyzes the epidemic spreading rules, and establishes an efficient equal distribution model of drugs in a broad sense. For multiple regions, in case of demand of drugs exceeding supply, the drugs shall be distributed according to the proportion of a total number of people in each region, the number of patients, the number of the isolated, and the number of deaths. It is necessary to simulate based on these four schemes to obtain simulation results. The results show that, when the drugs are distributed by the proportion of the number of deaths, it is optimal for controlling over epidemic situations.

  5. Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles

    CERN Document Server

    Vagne, Quentin

    2016-01-01

    The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we show that full maturation of membrane-bound compartments can be seen as the stochastic escape from a steady-state in which export is dominated by vesicular exchange. We show that full maturation can contribute a significant fraction of the total out-flux for small organelles such as endosomes and Golgi cisternae.

  6. Mechanistic model of radon-induced lung cancer risk at low exposure levels based on cellular alpha particle hits

    Energy Technology Data Exchange (ETDEWEB)

    Werner, Hofmann; Hatim, Fakir [Salzburg Univ., Div. of Physics and Biophysics, Dept. of Material Science (Austria); Lucia-Adina, Truta-Popa [Babes-Bolyai Univ., Faculty of Physics (Romania)

    2006-07-01

    To explore the role of the multiplicity of cellular hits by radon progeny alpha particles for lung cancer incidence, the number of single and multiple alpha particle hits were computed for basal and secretory cells in the bronchial epithelium of human airway bifurcations employing Monte Carlo methods. Hot spots of alpha particle hits were observed at the branching points of bronchial airway bifurcations, suggesting that multiple alpha particle hits may occur primarily at carinal ridges. Random alpha particle intersections of bronchial cells during a given exposure period, selected from a Poisson distribution, were simulated by an initiation-promotion model, based on experimentally observed cellular transformation and survival functions. To consider potential bystander effects, which have been observed in cellular in vitro studies, alpha particle interactions were also simulated for larger sensitive target volumes in bronchial epithelium, consisting of a collection of cells. Lung cancer risk simulations indicated that cancer induction for continuous exposures is related to the cycle time of an irradiated cell, thus exhibiting a distinct dose-rate effect. While the dominant role of single hits leads to a linear dose-response relationship at low radon exposure levels, predicted lung cancer risk for a collection of interacting cells exhibits a linear-quadratic response, suggesting that bystander effects, if operating at all under in vivo irradiations, may be restricted to a small number of adjacent cells. (author)

  7. Mechanistic model of radon-induced lung cancer risk at low exposure levels based on cellular alpha particle hits

    International Nuclear Information System (INIS)

    To explore the role of the multiplicity of cellular hits by radon progeny alpha particles for lung cancer incidence, the number of single and multiple alpha particle hits were computed for basal and secretory cells in the bronchial epithelium of human airway bifurcations employing Monte Carlo methods. Hot spots of alpha particle hits were observed at the branching points of bronchial airway bifurcations, suggesting that multiple alpha particle hits may occur primarily at carinal ridges. Random alpha particle intersections of bronchial cells during a given exposure period, selected from a Poisson distribution, were simulated by an initiation-promotion model, based on experimentally observed cellular transformation and survival functions. To consider potential bystander effects, which have been observed in cellular in vitro studies, alpha particle interactions were also simulated for larger sensitive target volumes in bronchial epithelium, consisting of a collection of cells. Lung cancer risk simulations indicated that cancer induction for continuous exposures is related to the cycle time of an irradiated cell, thus exhibiting a distinct dose-rate effect. While the dominant role of single hits leads to a linear dose-response relationship at low radon exposure levels, predicted lung cancer risk for a collection of interacting cells exhibits a linear-quadratic response, suggesting that bystander effects, if operating at all under in vivo irradiations, may be restricted to a small number of adjacent cells. (author)

  8. The 3′ Untranslated Region of the Rabies Virus Glycoprotein mRNA Specifically Interacts with Cellular PCBP2 Protein and Promotes Transcript Stability

    OpenAIRE

    Palusa, Saiprasad; Ndaluka, Christina; Bowen, Richard A.; Wilusz, Carol J.; Wilusz, Jeffrey

    2012-01-01

    Viral polymerase entry and pausing at intergenic junctions is predicted to lead to a defined polarity in the levels of rhabdovirus gene expression. Interestingly, we observed that the rabies virus glycoprotein mRNA is differentially over-expressed based on this model relative to other transcripts during infection of 293T cells. During infection, the rabies virus glycoprotein mRNA also selectively interacts with the cellular poly(rC)-binding protein 2 (PCBP2), a factor known to influence mRNA ...

  9. Mystery of the Toxic Flea Dip: An Interactive Approach to Teaching Aerobic Cellular Respiration

    Science.gov (United States)

    Baines, A. T.; McVey, M.; Rybarczyk, B.; Thompson, J. T.; Wilkins, H. R.

    2004-01-01

    We designed an interrupted case study to teach aerobic cellular respiration to major and nonmajor biology students. The case is based loosely on a real-life incident of rotenone poisoning. It places students in the role of a coroner who must determine the cause of death of the victim. The case is presented to the students in four parts. Each part…

  10. Designing and implementing a regional urban modeling system using the SLEUTH cellular urban model

    Science.gov (United States)

    Jantz, C.A.; Goetz, S.J.; Donato, D.; Claggett, P.

    2010-01-01

    This paper presents a fine-scale (30 meter resolution) regional land cover modeling system, based on the SLEUTH cellular automata model, that was developed for a 257000 km2 area comprising the Chesapeake Bay drainage basin in the eastern United States. As part of this effort, we developed a new version of the SLEUTH model (SLEUTH-3r), which introduces new functionality and fit metrics that substantially increase the performance and applicability of the model. In addition, we developed methods that expand the capability of SLEUTH to incorporate economic, cultural and policy information, opening up new avenues for the integration of SLEUTH with other land-change models. SLEUTH-3r is also more computationally efficient (by a factor of 5) and uses less memory (reduced 65%) than the original software. With the new version of SLEUTH, we were able to achieve high accuracies at both the aggregate level of 15 sub-regional modeling units and at finer scales. We present forecasts to 2030 of urban development under a current trends scenario across the entire Chesapeake Bay drainage basin, and three alternative scenarios for a sub-region within the Chesapeake Bay watershed to illustrate the new ability of SLEUTH-3r to generate forecasts across a broad range of conditions. ?? 2009 Elsevier Ltd.

  11. Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins

    OpenAIRE

    Cavaliere, Matteo; Sedwards, Sean

    2006-01-01

    Membrane systems were introduced as models of computation inspired by the structure and functioning of biological cells. Recently, membrane systems have also been shown to be suitable to model cellular processes. We introduce a new model called Membrane Systems with Peripheral and Integral Proteins. The model has compartments enclosed by membranes, floating objects, objects associated to the internal and external surfaces of the membranes and also objects integral to the membranes. The floati...

  12. Evaluation of BACE1 Silencing in Cellular Models

    Directory of Open Access Journals (Sweden)

    Barbara Nawrot

    2009-01-01

    Full Text Available Beta-secretase (BACE1 is the major enzyme participating in generation of toxic amyloid-beta (Aβ peptides, identified in amyloid plaques of Alzheimer's disease (AD brains. Its downregulation results in decreasing secretion of Aβ. Thus, BACE1 silencing by RNAi represents possible strategy for antiamyloid therapy in the treatment of AD. In this study, a series of newly designed sequences of synthetic and vector-encoded siRNAs (pSilencer, pcPURhU6, and lentivirus were tested against overexpressed and endogenous BACE1 in several cell lines and in adult neural progenitor cells, derived from rat hippocampus. SiRNAs active in human, mouse, and rat cell models were shown to diminish the level of BACE1. In HCN A94 cells, two BACE1-specific siRNAs did not alter the expression of genes of BACE2 and several selected genes involved in neurogenesis (Synapsin I, βIII-Tubulin, Calbidin, NeuroD1, GluR2, CREB, MeCP2, PKR, however, remarkable lowering of SCG10 mRNA, coding protein of stathmin family, important in the development of nervous system, was observed.

  13. Interactive Modelling of Molecular Structures

    Science.gov (United States)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  14. Optimized parallel computing for cellular automaton–finite element modeling of solidification grain structures

    International Nuclear Information System (INIS)

    A numerical implementation of a three-dimensional (3D) cellular automaton (CA)–finite element (FE) model has been developed for the prediction of solidification grain structures. For the first time, it relies on optimized parallel computation to solve industrial-scale problems (centimeter to meter long) while using a sufficiently small CA grid size to predict representative structures. Several algorithm modifications and strategies to maximize parallel efficiency are introduced. Improvements on a real case simulation are measured and discussed. The CA–FE implementation here is demonstrated using 32 computing units to predict grain structure in a 2.08 m × 0.382 m × 0.382 m ingot involving 4.9 billion cells and 1.6 million grains. These numerical improvements permit tracking of local changes in texture and grain size over real-cast parts while integrating interactions with macrosegregation, heat flow and fluid flow. Full 3D is essential in all these analyses, and can be dealt with successfully using the implementation presented here. (paper)

  15. Modeling mechanical behaviors of composites with various ratios of matrixeinclusion properties using movable cellular automaton method

    Institute of Scientific and Technical Information of China (English)

    A.Yu. SMOLIN; E.V. SHILKO; S.V. ASTAFUROV; I.S. KONOVALENKO; S.P. BUYAKOVA; S.G. PSAKHIE

    2015-01-01

    Two classes of composite materials are considered: classical metaleceramic composites with reinforcing hard inclusions as well as hard ceramics matrix with soft gel inclusions. Movable cellular automaton method is used for modeling the mechanical behaviors of such different heterogeneous materials. The method is based on particle approach and may be considered as a kind of discrete element method. The main feature of the method is the use of many-body forces of inter-element interaction within the formalism of simply deformable element approximation. It was shown that the strength of reinforcing particles and the width of particle-binder interphase boundaries had determining influence on the service characteristics of metaleceramic composite. In particular, the increasing of strength of carbide inclusions may lead to significant increase in the strength and ultimate strain of composite material. On the example of porous zirconia ceramics it was shown that the change in the mechanical properties of pore surface leads to the corresponding change in effective elastic modulus and strength limit of the ceramic sample. The less is the pore size, the more is this effect. The increase in the elastic properties of pore surface of ceramics may reduce its fracture energy.

  16. Discovering the cellular-localized functional modules and modular interactions in response to liver cancer

    Institute of Scientific and Technical Information of China (English)

    Zhu Jing; Guo Zheng; Yang Da; Zhang Min; Wang Jing; Wang Chenguang

    2008-01-01

    In this paper, we firstly identify the functional modules enriched with differentially expressed genes (DEGs) and characterized by biological processes in specific cellular locations, based on gene ontology (GO) and microarray data. Then, we further define and filter disease relevant signature modules according to the ranking of the disease discriminating abilities of the pre-selected functional modules. At last, we analyze the potential way by which they cooperate towards human disease. Application of the proposed method to the analysis of a liver cancer dataset shows that, using the same false discovery rate (FDR) threshold, we can find more biologically meaningful and detailed processes by using the cellular localization information. Some biological evidences support the relevancy of our biological modules to the disease mechanism.

  17. Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation.

    Science.gov (United States)

    Garn, Holger; Bahn, Sabine; Baune, Bernhard T; Binder, Elisabeth B; Bisgaard, Hans; Chatila, Talal A; Chavakis, Triantafyllos; Culmsee, Carsten; Dannlowski, Udo; Gay, Steffen; Gern, James; Haahtela, Tari; Kircher, Tilo; Müller-Ladner, Ulf; Neurath, Markus F; Preissner, Klaus T; Reinhardt, Christoph; Rook, Graham; Russell, Shannon; Schmeck, Bernd; Stappenbeck, Thaddeus; Steinhoff, Ulrich; van Os, Jim; Weiss, Scott; Zemlin, Michael; Renz, Harald

    2016-07-01

    Recent research indicates that chronic inflammatory diseases, including allergies and autoimmune and neuropsychiatric diseases, share common pathways of cellular and molecular dysregulation. It was the aim of the International von-Behring-Röntgen Symposium (October 16-18, 2014, in Marburg, Germany) to discuss recent developments in this field. These include a concept of biodiversity; the contribution of urbanization, lifestyle factors, and nutrition (eg, vitamin D); and new mechanisms of metabolic and immune dysregulation, such as extracellular and intracellular RNAs and cellular and mitochondrial stress. Epigenetic mechanisms contribute further to altered gene expression and therefore to the development of chronic inflammation. These novel findings provide the foundation for further development of preventive and therapeutic strategies. PMID:27373325

  18. Characterization of the Interaction of Lassa Fever Virus with Its Cellular Receptor α-Dystroglycan

    OpenAIRE

    Kunz, Stefan; Rojek, Jillian M.; Perez, Mar; Spiropoulou, Christina F.; Oldstone, Michael B. A.

    2005-01-01

    The cellular receptor for the Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) has recently been identified as α-dystroglycan (α-DG), a cell surface receptor that provides a molecular link between the extracellular matrix and the actin-based cytoskeleton. In the present study, we show that LFV binds to α-DG with high affinity in the low-nanomolar range. Recombinant vesicular stomatitis virus pseudotyped with LFV glycoprotein (GP) adopted the recepto...

  19. Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

    Directory of Open Access Journals (Sweden)

    Mondry Adrian

    2004-08-01

    Full Text Available Abstract Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods

  20. A robust cellular associative memory for pattern recognitions using composite trigonometric chaotic neuron models

    Directory of Open Access Journals (Sweden)

    Wimol San-Um

    2015-12-01

    Full Text Available This paper presents a robust cellular associative memory for pattern recognitions using composite trigonometric chaotic neuron models. Robust chaotic neurons are designed through a scan of positive Lyapunov Exponent (LE bifurcation structures, which indicate the quantitative measure of chaoticity for one-dimensional discrete-time dynamical systems. The proposed chaotic neuron model is a composite of sine and cosine chaotic maps, which are independent from the output activation function. Dynamics behaviors are demonstrated through bifurcation diagrams and LE-based bifurcation structures. An application to associative memories of binary patterns in Cellular Neural Networks (CNN topology is demonstrated using a signum output activation function. Examples of English alphabets are stored using symmetric auto-associative matrix of n-binary patterns. Simulation results have demonstrated that the cellular neural network can quickly and effectively restore the distorted pattern to expected information.

  1. Platinum nanozymes recover cellular ROS homeostasis in an oxidative stress-mediated disease model

    Science.gov (United States)

    Moglianetti, Mauro; de Luca, Elisa; Pedone, Deborah; Marotta, Roberto; Catelani, Tiziano; Sartori, Barbara; Amenitsch, Heinz; Retta, Saverio Francesco; Pompa, Pier Paolo

    2016-02-01

    In recent years, the use of nanomaterials as biomimetic enzymes has attracted great interest. In this work, we show the potential of biocompatible platinum nanoparticles (Pt NPs) as antioxidant nanozymes, which combine abundant cellular internalization and efficient scavenging activity of cellular reactive oxygen species (ROS), thus simultaneously integrating the functions of nanocarriers and antioxidant drugs. Careful toxicity assessment and intracellular tracking of Pt NPs proved their cytocompatibility and high cellular uptake, with compartmentalization within the endo/lysosomal vesicles. We have demonstrated that Pt NPs possess strong and broad antioxidant properties, acting as superoxide dismutase, catalase, and peroxidase enzymes, with similar or even superior performance than natural enzymes, along with higher adaptability to the changes in environmental conditions. We then exploited their potent activity as radical scavenging materials in a cellular model of an oxidative stress-related disorder, namely human Cerebral Cavernous Malformation (CCM) disease, which is associated with a significant increase in intracellular ROS levels. Noteworthily, we found that Pt nanozymes can efficiently reduce ROS levels, completely restoring the cellular physiological homeostasis.In recent years, the use of nanomaterials as biomimetic enzymes has attracted great interest. In this work, we show the potential of biocompatible platinum nanoparticles (Pt NPs) as antioxidant nanozymes, which combine abundant cellular internalization and efficient scavenging activity of cellular reactive oxygen species (ROS), thus simultaneously integrating the functions of nanocarriers and antioxidant drugs. Careful toxicity assessment and intracellular tracking of Pt NPs proved their cytocompatibility and high cellular uptake, with compartmentalization within the endo/lysosomal vesicles. We have demonstrated that Pt NPs possess strong and broad antioxidant properties, acting as superoxide

  2. Physiopathology of blood platelets: a model system for studies of cell-to-cell interaction. Progress report, November 1, 1979-October 31, 1980

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-01-01

    This report covers the studies on basic mechanisms of cellular interactions, utilizing platelets as a model system and, when possible, concentrating on the influence that environmental factors (nutritional, metabolic, cellular, immunologic and others) have on them. The four major sections include: platelet interaction with tumor cells; a model for the study of cell-to-cell interaction; interaction of platelets with vessel walls; and platelet interactions with immune proteins.

  3. Comparing the epidermal growth factor interaction with four different cell lines: intriguing effects imply strong dependency of cellular context.

    Directory of Open Access Journals (Sweden)

    Hanna Björkelund

    Full Text Available The interaction of the epidermal growth factor (EGF with its receptor (EGFR is known to be complex, and the common over-expression of EGF receptor family members in a multitude of tumors makes it important to decipher this interaction and the following signaling pathways. We have investigated the affinity and kinetics of (125I-EGF binding to EGFR in four human tumor cell lines, each using four culturing conditions, in real time by use of LigandTracer®.Highly repeatable and precise measurements show that the overall apparent affinity of the (125I-EGF - EGFR interaction is greatly dependent on cell line at normal culturing conditions, ranging from K(D ≈ 200 pM on SKBR3 cells to K(D≈8 nM on A431 cells. The (125I-EGF - EGFR binding curves (irrespective of cell line have strong signs of multiple simultaneous interactions. Furthermore, for the cell lines A431 and SKOV3, gefitinib treatment increases the (125I-EGF - EGFR affinity, in particular when the cells are starved. The (125I-EGF - EGFR interaction on cell line U343 is sensitive to starvation while as on SKBR3 it is insensitive to gefitinib and starvation.The intriguing pattern of the binding characteristics proves that the cellular context is important when deciphering how EGF interacts with EGFR. From a general perspective, care is advisable when generalizing ligand-receptor interaction results across multiple cell-lines.

  4. Accumulated SET protein up-regulates and interacts with hnRNPK, increasing its binding to nucleic acids, the Bcl-xS repression, and cellular proliferation

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Luciana O.; Garcia, Cristiana B.; Matos-Silva, Flavia A. [Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP (Brazil); Curti, Carlos [Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP (Brazil); Leopoldino, Andréia M., E-mail: andreiaml@usp.br [Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP (Brazil)

    2014-02-28

    Highlights: • hnRNPK is a new target of SET. • SET regulates hnRNPK. • SET and hnRNPK accumulation promotes tumorigenesis. • SET accumulation is a potential model to study genes regulated by SET-hnRNPK. - Abstract: SET and hnRNPK are proteins involved in gene expression and regulation of cellular signaling. We previously demonstrated that SET accumulates in head and neck squamous cell carcinoma (HNSCC); hnRNPK is a prognostic marker in cancer. Here, we postulate that SET and hnRNPK proteins interact to promote tumorigenesis. We performed studies in HEK293 and HNSCC (HN6, HN12, and HN13) cell lines with SET/hnRNPK overexpression and knockdown, respectively. We found that SET and/or hnRNPK protein accumulation increased cellular proliferation. SET accumulation up-regulated hnRNPK mRNA and total/phosphorylated protein, promoted hnRNPK nuclear location, and reduced Bcl-x mRNA levels. SET protein directly interacted with hnRNPK, increasing both its binding to nucleic acids and Bcl-xS repression. We propose that hnRNPK should be a new target of SET and that SET–hnRNPK interaction, in turn, has potential implications in cell survival and malignant transformation.

  5. A cellular automata model for population expansion of Spartina alterniflora at Jiuduansha Shoals, Shanghai, China

    Science.gov (United States)

    Huang, Hua-mei; Zhang, Li-quan; Guan, Yu-juan; Wang, Dong-hui

    2008-03-01

    Biological invasion has received considerable attention recently because of increasing impacts on local ecosystems. Expansion of Spartina alterniflora, a non-native species, on the intertidal mudflats of Jiuduansha Shoals at the Yangtze River Estuary is a prime example of a spatially-structured invasion in a relatively simple habitat, for which strategic control efforts can be modeled and applied. Here, we developed a Cellular Automata (CA) model, in conjunction with Remote Sensing and Geographical Information Systems, to simulate the expanding process of S. alterniflora for a period of 8 years after being introduced to the new shoals, and to study the interactions between spatial pattern and ecosystem processes for the saltmarsh vegetation. The results showed that the CA model could simulate the population dynamics of S. alterniflora and Phragmites australis on the Jiuduansha Shoals successfully. The results strongly support the hypothesis of space pre-emption as well as range expansion with simple advancing wave fronts for these two species. In the Yangtze River Estuary, the native species P. australis shares the same niche with the exotic species S. alterniflora. However, the range expansion rate of P. australis was much slower than that of S. alterniflora. With the accretion of the Jiuduansha Shoals due to the large quantity of sediments deposited by the Yangtze River, a rapid range expansion of S. alterniflora is predicted to last for a long period into future. This study indicated the potential for this approach to provide valuable insights into population and community ecology of invasive species, which could be very important for wetland biodiversity conservation and resource management in the Yangtze River Estuary and other such impacted areas.

  6. Towards Inter- and Intra- Cellular Protein Interaction Analysis: Applying the Betweenness Centrality Graph Measure for Node Importance

    Science.gov (United States)

    Barton, Alan J.; Haqqani, Arsalan S.

    2011-11-01

    Three public biological network data sets (KEGG, GeneRIF and Reactome) are collected and described. Two problems are investigated (inter- and intra- cellular interactions) via augmentation of the collected networks to the problem specific data. Results include an estimate of the importance of proteins for the interaction of inflammatory cells with the blood-brain barrier via the computation of Betweenness Centrality. Subsequently, the interactions may be validated from a number of differing perspectives; including comparison with (i) existing biological results, (ii) the literature, and (iii) new hypothesis driven biological experiments. Novel therapeutic and diagnostic targets for inhibiting inflammation at the blood-brain barrier in a number of brain diseases including Alzheimer's disease, stroke and multiple sclerosis are possible. In addition, this methodology may also be applicable towards investigating the breast cancer tumour microenvironment.

  7. Multifunction Co-culture Model for Evaluating Cell–Cell Interactions

    OpenAIRE

    Bogdanowicz, Danielle R.; Lu, Helen H.

    2014-01-01

    Interactions within the same cell population (homotypic) and between different cell types (heterotypic) are essential for tissue development, repair, and homeostasis. To elucidate the underlying mechanisms of these cellular interactions, co-culture models have been used extensively to investigate the role of cell–cell physical contact, autocrine and/or paracrine interactions on cell function, as well as stem cell differentiation. Specifically, the mixed co-culture model is often optimal for i...

  8. fA cellular automaton model of crystalline cellulose hydrolysis by cellulases

    Directory of Open Access Journals (Sweden)

    Little Bryce A

    2011-10-01

    Full Text Available Abstract Background Cellulose from plant biomass is an abundant, renewable material which could be a major feedstock for low emissions transport fuels such as cellulosic ethanol. Cellulase enzymes that break down cellulose into fermentable sugars are composed of different types - cellobiohydrolases I and II, endoglucanase and β-glucosidase - with separate functions. They form a complex interacting network between themselves, soluble hydrolysis product molecules, solution and solid phase substrates and inhibitors. There have been many models proposed for enzymatic saccharification however none have yet employed a cellular automaton approach, which allows important phenomena, such as enzyme crowding on the surface of solid substrates, denaturation and substrate inhibition, to be considered in the model. Results The Cellulase 4D model was developed de novo taking into account the size and composition of the substrate and surface-acting enzymes were ascribed behaviors based on their movements, catalytic activities and rates, affinity for, and potential for crowding of, the cellulose surface, substrates and inhibitors, and denaturation rates. A basic case modeled on literature-derived parameters obtained from Trichoderma reesei cellulases resulted in cellulose hydrolysis curves that closely matched curves obtained from published experimental data. Scenarios were tested in the model, which included variation of enzyme loadings, adsorption strengths of surface acting enzymes and reaction periods, and the effect on saccharide production over time was assessed. The model simulations indicated an optimal enzyme loading of between 0.5 and 2 of the base case concentrations where a balance was obtained between enzyme crowding on the cellulose crystal, and that the affinities of enzymes for the cellulose surface had a large effect on cellulose hydrolysis. In addition, improvements to the cellobiohydrolase I activity period substantially improved overall

  9. Color Graphs: An Efficient Model For Two-Dimensional Cellular Automata Linear Rules

    CERN Document Server

    Nayak, Birendra Kumar; Rout, Sushant Kumar

    2008-01-01

    Two-dimensional nine neighbor hood rectangular Cellular Automata rules can be modeled using many different techniques like Rule matrices, State Transition Diagrams, Boolean functions, Algebraic Normal Form etc. In this paper, a new model is introduced using color graphs to model all the 512 linear rules. The graph theoretic properties therefore studied in this paper simplifies the analysis of all linear rules in comparison with other ways of its study.

  10. A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling

    OpenAIRE

    Xiaonian Shan; Zhibin Li; Xiaohong Chen; Jianhong Ye

    2015-01-01

    Several previous studies have used the Cellular Automaton (CA) for the modeling of bicycle traffic flow. However, previous CA models have several limitations, resulting in differences between the simulated and the observed traffic flow features. The primary objective of this study is to propose a modified CA model for simulating the characteristics of mixed bicycle traffic flow. Field data were collected on physically separated bicycle path in Shanghai, China, and were used to calibrate the C...

  11. Lattice gas cellular automata model for rippling and aggregation in myxobacteria

    OpenAIRE

    Alber, Mark S.; Jiang, Yi; Kiskowski, Maria A.

    2004-01-01

    A lattice-gas cellular automaton (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions f...

  12. An analytical model for interactive failures

    International Nuclear Information System (INIS)

    In some systems, failures of certain components can interact with each other, and accelerate the failure rates of these components. These failures are defined as interactive failure. Interactive failure is a prevalent cause of failure associated with complex systems, particularly in mechanical systems. The failure risk of an asset will be underestimated if the interactive effect is ignored. When failure risk is assessed, interactive failures of an asset need to be considered. However, the literature is silent on previous research work in this field. This paper introduces the concepts of interactive failure, develops an analytical model to analyse this type of failure quantitatively, and verifies the model using case studies and experiments

  13. Embryonic stem cells as an ectodermal cellular model of human p63-related dysplasia syndromes.

    NARCIS (Netherlands)

    Rostagno, P.; Wolchinsky, Z.; Vigano, A.M.; Shivtiel, S.; Zhou, H.; Bokhoven, J.H.L.M. van; Ferone, G.; Missero, C.; Mantovani, R.; Aberdam, D.; Virolle, T.

    2010-01-01

    Heterozygous mutations in the TP63 transcription factor underlie the molecular basis of several similar autosomal dominant ectodermal dysplasia (ED) syndromes. Here we provide a novel cellular model derived from embryonic stem (ES) cells that recapitulates in vitro the main steps of embryonic skin d

  14. An agent-based model of cellular dynamics and circadian variability in human endotoxemia.

    Directory of Open Access Journals (Sweden)

    Tung T Nguyen

    Full Text Available As cellular variability and circadian rhythmicity play critical roles in immune and inflammatory responses, we present in this study an agent-based model of human endotoxemia to examine the interplay between circadian controls, cellular variability and stochastic dynamics of inflammatory cytokines. The model is qualitatively validated by its ability to reproduce circadian dynamics of inflammatory mediators and critical inflammatory responses after endotoxin administration in vivo. Novel computational concepts are proposed to characterize the cellular variability and synchronization of inflammatory cytokines in a population of heterogeneous leukocytes. Our results suggest that there is a decrease in cell-to-cell variability of inflammatory cytokines while their synchronization is increased after endotoxin challenge. Model parameters that are responsible for IκB production stimulated by NFκB activation and for the production of anti-inflammatory cytokines have large impacts on system behaviors. Additionally, examining time-dependent systemic responses revealed that the system is least vulnerable to endotoxin in the early morning and most vulnerable around midnight. Although much remains to be explored, proposed computational concepts and the model we have pioneered will provide important insights for future investigations and extensions, especially for single-cell studies to discover how cellular variability contributes to clinical implications.

  15. A material optimization model to approximate energy bounds for cellular materials under multiload conditions

    DEFF Research Database (Denmark)

    Guedes, J.M.; Rodrigues, H.C.; Bendsøe, Martin P.

    2003-01-01

    This paper describes a computational model, based on inverse homogenization and topology design, for approximating energy bounds for two-phase composites under multiple load cases. The approach allows for the identification of possible single-scale cellular materials that give rise to the optimal...

  16. Model Perubahan Penggunaan Lahan Menggunakan Cellular Automata-Markov Chain di Kawasan Mamminasata

    OpenAIRE

    Vera Damayanti Peruge, Tiur

    2012-01-01

    Telah dilakukan penelitian tentang perubahan penggunaan lahan di kawasan Mamminasata menggunakan model Cellular Automata-Markov Chain. Tujuan dari penelitian ini adalah menganalisis perubahan penggunaan lahan melalui peta penggunaan lahan kawasan Mamminasata tahun 2004 dan 2009 untuk memperoleh penggunaan lahan tahun 2012 berbasis Markov Chain dengan analisis probabilitas transisi Markov. Hasil analisis yang diperoleh dilakukan validasi dengan validasi Kappa m...

  17. Modelling Iron-Bentonite Interactions

    Science.gov (United States)

    Watson, C.; Savage, D.; Benbow, S.; Wilson, J.

    2009-04-01

    The presence of both iron canisters and bentonitic clay in some engineered barrier system (EBS) designs for the geological disposal of high-level radioactive wastes creates the potential for chemical interactions which may impact upon the long-term performance of the clay as a barrier to radionuclide migration. Flooding of potential radionuclide sorption sites on the clay by ferrous ions and conversion of clay to non-swelling sheet silicates (e.g. berthierine) are two possible outcomes deleterious to long-term performance. Laboratory experimental studies of the corrosion of iron in clay show that corrosion product layers are generally thin ( 250 °C) are dominated by chlorite, whereas lower temperatures produce berthierine, odinite, cronstedtite, or Fe-rich smectite. Unfortunately, the inevitable short-term nature of laboratory experimental studies introduces issues of metastability and kinetics. The sequential formation in time of minerals in natural systems often produces the formation of phases not predicted by equilibrium thermodynamics. Evidence from analogous natural systems suggests that the sequence of alteration of clay by Fe-rich fluids will proceed via an Ostwald step sequence. The computer code, QPAC, has been modified to incorporate processes of nucleation, growth, precursor cannibalisation, and Ostwald ripening to address the issues of the slow growth of bentonite alteration products. This, together with inclusion of processes of iron corrosion and diffusion, has enabled investigation of a representative model of the alteration of bentonite in a typical EBS environment. Simulations with fixed mineral surface areas show that berthierine dominates the solid product assemblage, with siderite replacing it at simulation times greater than 10 000 years. Simulations with time-dependent mineral surface areas show a sequence of solid alteration products, described by: magnetite -> cronstedtite -> berthierine -> chlorite. Using plausible estimates of mineral

  18. Cellular and molecular modifier pathways in tauopathies: the big picture from screening invertebrate models.

    Science.gov (United States)

    Hannan, Shabab B; Dräger, Nina M; Rasse, Tobias M; Voigt, Aaron; Jahn, Thomas R

    2016-04-01

    Abnormal tau accumulations were observed and documented in post-mortem brains of patients affected by Alzheimer's disease (AD) long before the identification of mutations in the Microtubule-associated protein tau (MAPT) gene, encoding the tau protein, in a different neurodegenerative disease called Frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). The discovery of mutations in the MAPT gene associated with FTDP-17 highlighted that dysfunctions in tau alone are sufficient to cause neurodegeneration. Invertebrate models have been diligently utilized in investigating tauopathies, contributing to the understanding of cellular and molecular pathways involved in disease etiology. An important discovery came with the demonstration that over-expression of human tau in Drosophila leads to premature mortality and neuronal dysfunction including neurodegeneration, recapitulating some key neuropathological features of the human disease. The simplicity of handling invertebrate models combined with the availability of a diverse range of experimental resources make these models, in particular Drosophila a powerful invertebrate screening tool. Consequently, several large-scale screens have been performed using Drosophila, to identify modifiers of tau toxicity. The screens have revealed not only common cellular and molecular pathways, but in some instances the same modifier has been independently identified in two or more screens suggesting a possible role for these modifiers in regulating tau toxicity. The purpose of this review is to discuss the genetic modifier screens on tauopathies performed in Drosophila and C. elegans models, and to highlight the common cellular and molecular pathways that have emerged from these studies. Here, we summarize results of tau toxicity screens providing mechanistic insights into pathological alterations in tauopathies. Key pathways or modifiers that have been identified are associated with a broad range of processes

  19. Computational Modelling of the Structural Integrity following Mass-Loss in Polymeric Charred Cellular Solids

    Directory of Open Access Journals (Sweden)

    J. P. M. Whitty

    2014-01-01

    Full Text Available A novel computational technique is presented for embedding mass-loss due to burning into the ANSYS finite element modelling code. The approaches employ a range of computational modelling methods in order to provide more complete theoretical treatment of thermoelasticity absent from the literature for over six decades. Techniques are employed to evaluate structural integrity (namely, elastic moduli, Poisson’s ratios, and compressive brittle strength of honeycomb systems known to approximate three-dimensional cellular chars. That is, reducing the mass of diagonal ribs and both diagonal-plus-vertical ribs simultaneously show rapid decreases in the structural integrity of both conventional and reentrant (auxetic, i.e., possessing a negative Poisson’s ratio honeycombs. On the other hand, reducing only the vertical ribs shows initially modest reductions in such properties, followed by catastrophic failure of the material system. Calculations of thermal stress distributions indicate that in all cases the total stress is reduced in reentrant (auxetic cellular solids. This indicates that conventional cellular solids are expected to fail before their auxetic counterparts. Furthermore, both analytical and FE modelling predictions of the brittle crush strength of both auxteic and conventional cellular solids show a relationship with structural stiffness.

  20. Modeling of solidification grain structure for Ti-45%Al alloy ingot by cellular automaton

    Institute of Scientific and Technical Information of China (English)

    WU Shi-ping; LIU Dong-rong; GUO Jing-jie; FU Heng-zhi

    2005-01-01

    A cellular automaton model for simulating grain structure formation during solidification processes of Ti45%Al(mole fraction) alloy ingot was developed, based on finite differential method for macroscopic modeling of heat transfer and a cellular automaton technique for microscopic modeling of nucleation, growth, solute redistribution and solute diffusion. The relation between the growth velocity of a dendrite tip and the local undercooling,which consists of constitutional, thermal, curvature and attachment kinetics undercooling is calculated according to the Kurz-Giovanola-Trivedi model. The effect of solidification contraction is taken into consideration. The influence of process variables upon the resultant grain structures was investigated. Special moving allocation technique was designed to minimize the computation time and memory size associated with a large number of cells. The predicted grain structures are in good agreement with the experimental results.

  1. Genome-wide Mapping of Cellular Protein-RNA Interactions Enabled by Chemical Crosslinking

    Institute of Scientific and Technical Information of China (English)

    Xiaoyu Li; Jinghui Song; Chengqi Yi

    2014-01-01

    RNA-protein interactions influence many biological processes. Identifying the binding sites of RNA-binding proteins (RBPs) remains one of the most fundamental and important chal-lenges to the studies of such interactions. Capturing RNA and RBPs via chemical crosslinking allows stringent purification procedures that significantly remove the non-specific RNA and protein interactions. Two major types of chemical crosslinking strategies have been developed to date, i.e., UV-enabled crosslinking and enzymatic mechanism-based covalent capture. In this review, we com-pare such strategies and their current applications, with an emphasis on the technologies themselves rather than the biology that has been revealed. We hope such methods could benefit broader audi-ence and also urge for the development of new methods to study RNA RBP interactions.

  2. Preparation of oligodeoxynucleotide encapsulated cationic liposomes and release study with models of cellular membranes

    OpenAIRE

    Tamaddon AM.; Hosseini-Shirazi F.; Moghimi HR

    2007-01-01

    Cationic liposomes are used for cellular delivery of antisense oligodeoxynucleotide (AsODN), where release of encapsulated AsODN is mainly controlled by endocytosis and fusion mechanisms. In this investigation, it was tried to model such a release process that is difficult to evaluate in cell culture. For this purpose, an AsODN model (against protein kinase C-α) was encapsulated in a DODAP-containing cationic liposome and evaluated for size, zeta-potential, encapsulation and ODN stab...

  3. Modeling of aluminum-silicon irregular eutectic growth by cellular automaton model

    Directory of Open Access Journals (Sweden)

    Rui Chen

    2016-03-01

    Full Text Available Due to the extensive application of Al-Si alloys in the automotive and aerospace industries as structural components, an understanding of their microstructural formation, such as dendrite and (Al+Si eutectic, is of great importance to control the desirable microstructure, so as to modify the performance of castings. Since previous major themes of microstructural simulation are dendrite and regular eutectic growth, few efforts have been paid to simulate the irregular eutectic growth. Therefore, a multiphase cellular automaton (CA model is developed and applied to simulate the time-dependent Al-Si irregular eutectic growth. Prior to model establishment, related experiments were carried out to investigate the influence of cooling rate and Sr modification on the growth of eutectic Si. This CA model incorporates several aspects, including growth algorithms and nucleation criterion, to achieve the competitive and cooperative growth mechanism for nonfaceted-faceted Al-Si irregular eutectic. The growth kinetics considers thermal undercooling, constitutional undercooling, and curvature undercooling, as well as the anisotropic characteristic of eutectic Si growth. The capturing rule takes into account the effects of modification on the silicon growth behaviors. The simulated results indicate that for unmodified alloy, the higher eutectic undercooling results in the higher eutectic growth velocity, and a more refined eutectic microstructure as well as narrower eutectic lamellar spacing. For modified alloy, the eutectic silicon tends to be obvious fibrous morphology and the morphology of eutectic Si is determined by both chemical modifier and cooling rate. The predicted microstructure of Al-7Si alloy under different solidification conditions shows that this proposed model can successfully reproduce both dendrite and eutectic microstructures.

  4. The critical properties of the agent-based model with environmental-economic interactions

    CERN Document Server

    Kuscsik, Z; Horváth, D

    2007-01-01

    The steady-state and nonequilibrium properties of the model of environmental-economic interactions are studied. The interacting heterogeneous agents are simulated on the platform of the emission dynamics of cellular automaton. The model possess the discontinuous transition between the safe and catastrophic ecology. Right at the critical line, the broad-scale power-law distributions of emission rates have been identified. Their relationship to Zipf's law and models of self-organized criticality is discussed.

  5. The telomeric protein AKTIP interacts with A- and B-type lamins and is involved in regulation of cellular senescence

    Science.gov (United States)

    Burla, Romina; Carcuro, Mariateresa; Torre, Mattia La; Fratini, Federica; Crescenzi, Marco; D'Apice, Maria Rosaria; Spitalieri, Paola; Raffa, Grazia Daniela; Astrologo, Letizia; Lattanzi, Giovanna; Cundari, Enrico; Raimondo, Domenico; Biroccio, Annamaria; Gatti, Maurizio

    2016-01-01

    AKTIP is a shelterin-interacting protein required for replication of telomeric DNA. Here, we show that AKTIP biochemically interacts with A- and B-type lamins and affects lamin A, but not lamin C or B, expression. In interphase cells, AKTIP localizes at the nuclear rim and in discrete regions of the nucleoplasm just like lamins. Double immunostaining revealed that AKTIP partially co-localizes with lamin B1 and lamin A/C in interphase cells, and that proper AKTIP localization requires functional lamin A. In mitotic cells, AKTIP is enriched at the spindle poles and at the midbody of late telophase cells similar to lamin B1. AKTIP-depleted cells show senescence-associated markers and recapitulate several aspects of the progeroid phenotype. Collectively, our results indicate that AKTIP is a new player in lamin-related processes, including those that govern nuclear architecture, telomere homeostasis and cellular senescence. PMID:27512140

  6. GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Brian; Ebrahim, Ali; Metz, Thomas O.; Adkins, Joshua N.; Palsson, Bernard O.; Hyduke, Daniel R.

    2013-11-15

    Motivation: Genome-scale metabolic models have been used extensively to investigate alterations in cellular metabolism. The accuracy of these models to represent cellular metabolism in specific conditions has been improved by constraining the model with omics data sources. However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been reported. Results: GIMMME (Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression) is an algorithm that enables the development of condition-specific models based on an objective function, transcriptomics, and intracellular metabolomics data. GIMMME establishes metabolite utilization requirements with metabolomics data, uses model-paired transcriptomics data to find experimentally supported solutions, and also provides calculations of the turnover (production / consumption) flux of metabolites. GIMMME was employed to investigate the effects of integrating additional omics datasets to create increasingly constrained solution spaces of Salmonella Typhimurium metabolism during growth in both rich and virulence media. This integration proved to be informative and resulted in a requirement of additional active reactions (12 in each case) or metabolites (26 or 29, respectively). The addition of constraints from transcriptomics also impacted the allowed solution space, and the cellular metabolites with turnover fluxes that were necessarily altered by the change in conditions increased from 118 to 271 of 1397. Availability: GIMMME has been implemented in Python and requires a COBRApy 0.2.x. The algorithm and sample data described here are freely available at: http://opencobra.sourceforge.net/

  7. Cellular immunity and pathogen strategies in combative interactions involving Drosophila hosts and their endoparasitic wasps

    Directory of Open Access Journals (Sweden)

    AJ Nappi

    2010-09-01

    Full Text Available Various cellular innate immune responses protect invertebrates from attack by eukaryotic pathogens. In insects, assessments of the factor(s causing, or contributing to, pathogen mortality have long considered as toxic components certain molecules associated with enzyme-mediated melanogenesis. In Drosophila hosts, observations that have prompted additional or alternative considerations are those that document either the survival of certain endoparasitic wasps despite melanotic encapsulation, or the destruction of the parasite with no evidence of this type of host response. Investigations of the production of some reactive intermediates of oxygen and nitrogen during infection provide a basis for proposing that these molecules constitute important elements of the immune arsenal of Drosophila. Studies of the target specificity of virulence factors injected by female wasps during infection that suppress the host immune response will likely facilitate identification of the toxic host molecules, and contribute to a more detailed understanding of the cell-signaling pathways that regulate their synthesis.

  8. Cellular interactions via conditioned media induce in vivo nephron generation from tubular epithelial cells or mesenchymal stem cells

    International Nuclear Information System (INIS)

    Highlights: •We have attempted in vivo nephron generation using conditioned media. •Vascular and tubular cells do cross-talks on cell proliferation and tubular changes. •Tubular cells suppress these changes in mesenchymal stem cells. •Tubular cells differentiate mesenchymal stem cells into tubular cells. •Nephrons can be created from implanted tubular cells or mesenchymal stem cells. -- Abstract: There are some successful reports of kidney generation by utilizing the natural course of kidney development, namely, the use of an artificially treated metanephros, blastocyst or ureteric bud. Under a novel concept of cellular interactions via conditioned media (CMs), we have attempted in vivo nephron generation from tubular epithelial cells (TECs) or mesenchymal stem cells (MSCs). Here we used 10× CMs of vascular endothelial cells (VECs) and TECs, which is the first to introduce a CM into the field of organ regeneration. We first present stimulative cross-talks induced by these CMs between VECs and TECs on cell proliferation and morphological changes. In MSCs, TEC-CM suppressed these changes, however, induced cytokeratin expression, indicating the differentiation of MSCs into TECs. As a result, glomerular and tubular structures were created following the implantation of TECs or MSCs with both CMs. Our findings suggest that the cellular interactions via CMs might induce in vivo nephron generation from TECs or MSCs. As a promoting factor, CMs could also be applied to the regeneration of other organs and tissues

  9. Cellular interactions via conditioned media induce in vivo nephron generation from tubular epithelial cells or mesenchymal stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Machiguchi, Toshihiko, E-mail: machiguchi.toshihiko.23u@st.kyoto-u.ac.jp; Nakamura, Tatsuo, E-mail: nakamura@frontier.kyoto-u.ac.jp

    2013-06-07

    Highlights: •We have attempted in vivo nephron generation using conditioned media. •Vascular and tubular cells do cross-talks on cell proliferation and tubular changes. •Tubular cells suppress these changes in mesenchymal stem cells. •Tubular cells differentiate mesenchymal stem cells into tubular cells. •Nephrons can be created from implanted tubular cells or mesenchymal stem cells. -- Abstract: There are some successful reports of kidney generation by utilizing the natural course of kidney development, namely, the use of an artificially treated metanephros, blastocyst or ureteric bud. Under a novel concept of cellular interactions via conditioned media (CMs), we have attempted in vivo nephron generation from tubular epithelial cells (TECs) or mesenchymal stem cells (MSCs). Here we used 10× CMs of vascular endothelial cells (VECs) and TECs, which is the first to introduce a CM into the field of organ regeneration. We first present stimulative cross-talks induced by these CMs between VECs and TECs on cell proliferation and morphological changes. In MSCs, TEC-CM suppressed these changes, however, induced cytokeratin expression, indicating the differentiation of MSCs into TECs. As a result, glomerular and tubular structures were created following the implantation of TECs or MSCs with both CMs. Our findings suggest that the cellular interactions via CMs might induce in vivo nephron generation from TECs or MSCs. As a promoting factor, CMs could also be applied to the regeneration of other organs and tissues.

  10. Semantic models for adaptive interactive systems

    CERN Document Server

    Hussein, Tim; Lukosch, Stephan; Ziegler, Jürgen; Calvary, Gaëlle

    2013-01-01

    Providing insights into methodologies for designing adaptive systems based on semantic data, and introducing semantic models that can be used for building interactive systems, this book showcases many of the applications made possible by the use of semantic models.Ontologies may enhance the functional coverage of an interactive system as well as its visualization and interaction capabilities in various ways. Semantic models can also contribute to bridging gaps; for example, between user models, context-aware interfaces, and model-driven UI generation. There is considerable potential for using

  11. Independent pair parton interactions-model of hadron interactions

    OpenAIRE

    Dremin, I. M.; Nechitailo, V. A.

    2004-01-01

    A model of independent pair parton interactions is proposed, according to which, hadron interactions are represented by a set of independent binary parton collisions. The final multiplicity distribution is described by a convolution of the negative binomial distributions in each of the partonic collisions. As a result, it is given by a weighted sum of negative binomial distributions with parameters multiplied by the number of active pairs. Its shape and moments are considered. Experimental da...

  12. Effect of self-interaction on the phase diagram of a Gibbs-like measure derived by a reversible Probabilistic Cellular Automata

    International Nuclear Information System (INIS)

    Cellular Automata are discrete-time dynamical systems on a spatially extended discrete space which provide paradigmatic examples of nonlinear phenomena. Their stochastic generalizations, i.e., Probabilistic Cellular Automata (PCA), are discrete time Markov chains on lattice with finite single-cell states whose distinguishing feature is the parallel character of the updating rule. We study the ground states of the Hamiltonian and the low-temperature phase diagram of the related Gibbs measure naturally associated with a class of reversible PCA, called the cross PCA. In such a model the updating rule of a cell depends indeed only on the status of the five cells forming a cross centered at the original cell itself. In particular, it depends on the value of the center spin (self-interaction). The goal of the paper is that of investigating the role played by the self-interaction parameter in connection with the ground states of the Hamiltonian and the low-temperature phase diagram of the Gibbs measure associated with this particular PCA

  13. Magneto-optical cellular chip model for intracellular orientational-dynamic-activity detection

    Science.gov (United States)

    Miyashita, Y.; Iwasaka, M.; Kurita, S.; Owada, N.

    2012-04-01

    In the present study, a magneto-optical cellular chip model (MoCCM) was developed to detect intracellular dynamics in macromolecules by using magneto-optical effects. For the purpose of cell-measurement under strong static magnetic fields of up to 10 T, we constructed a cellular chip model, which was a thin glass plate with a well for a cell culture. A cell line of osteoblast MC3T3-E1 was incubated in the glass well, and the well, 0.3 mm in depth, was sealed by a cover glass when the MoCCM was set in a fiber optic system. An initial intensity change of the polarized light transmission, which dispersed perpendicular to the cell's attaching surface, was collected for 10 to 60 min, and then magnetic fields were applied parallel and perpendicular to the surface and light direction, respectively. The magnetic birefringence signals that originated from the magnetic orientation of intracellular molecules such as cytoskeletons apparently appeared when the magnetic fields were constant at 10 T. A statistical analysis with 15 experiments confirmed that the cellular components under 10 T magnetic fields caused a stronger alignment, which was transferred into polarizing light intensity that increased more than the case before exposure. Cellular conditions such as generation and cell density affected the magnetic birefringence signals.

  14. Modeling of time-dose-LET effects in the cellular response to radiation

    International Nuclear Information System (INIS)

    This work is dedicated to the elucidation of time-dose- and if applicable linear energy transfer (LET) effects in the cellular response to ion or photon radiation. In particular, the common concept of the Local Effect Model (LEM) and the Giant Loop Binary Lesion (GLOBLE) model, which explains cell survival probabilities on the hand of clustering of double-strand breaks (DSB) in micrometer-sized sub-structural units of the DNA, was investigated with regard to temporal aspects. In previous studies with the LEM and GLOBLE model, it has been demonstrated that the definition of two lesion classes, characterized by single or multiple DSB in a DNA giant loop, with two repair fidelities is adequate to comprehensively describe the dose dependence of the cellular response to instantaneous photon irradiation or ion irradiation with varying LET. Furthermore, with the GLOBLE model for photon radiation, it has been shown that the assignment of two repair time scales to the two lesion classes allows to adequately reproduce time-dose effects after photon irradiation with an arbitrary constant dose-rate. In this work, the results of four projects that strengthen the mechanistic consistency and the practical applicability of the LEM and GLOBLE model will be presented. First, it was found that the GLOBLE model is applicable to describe time-dose effects in the cellular response to two split photon doses and in the occurrence of deterministic radiation effects. Second, in a comparison of ten models for the temporal course of DSB rejoining, it was revealed that a bi-exponential approach, as suggested by the LEM and GLOBLE model, finds a relatively large support by 61 experimental data sets. Third, in a comparison of four kinetic photon cell survival models that was based on fits to 13 dose-rate experiments, it was shown that the GLOBLE model performs well with respect to e.g. accuracy, parsimony, reliability and other factors that characterize a good approach. Last but not least, the

  15. Modeling of time-dose-LET effects in the cellular response to radiation

    Energy Technology Data Exchange (ETDEWEB)

    Herr, Lisa Antje

    2015-07-20

    This work is dedicated to the elucidation of time-dose- and if applicable linear energy transfer (LET) effects in the cellular response to ion or photon radiation. In particular, the common concept of the Local Effect Model (LEM) and the Giant Loop Binary Lesion (GLOBLE) model, which explains cell survival probabilities on the hand of clustering of double-strand breaks (DSB) in micrometer-sized sub-structural units of the DNA, was investigated with regard to temporal aspects. In previous studies with the LEM and GLOBLE model, it has been demonstrated that the definition of two lesion classes, characterized by single or multiple DSB in a DNA giant loop, with two repair fidelities is adequate to comprehensively describe the dose dependence of the cellular response to instantaneous photon irradiation or ion irradiation with varying LET. Furthermore, with the GLOBLE model for photon radiation, it has been shown that the assignment of two repair time scales to the two lesion classes allows to adequately reproduce time-dose effects after photon irradiation with an arbitrary constant dose-rate. In this work, the results of four projects that strengthen the mechanistic consistency and the practical applicability of the LEM and GLOBLE model will be presented. First, it was found that the GLOBLE model is applicable to describe time-dose effects in the cellular response to two split photon doses and in the occurrence of deterministic radiation effects. Second, in a comparison of ten models for the temporal course of DSB rejoining, it was revealed that a bi-exponential approach, as suggested by the LEM and GLOBLE model, finds a relatively large support by 61 experimental data sets. Third, in a comparison of four kinetic photon cell survival models that was based on fits to 13 dose-rate experiments, it was shown that the GLOBLE model performs well with respect to e.g. accuracy, parsimony, reliability and other factors that characterize a good approach. Last but not least, the

  16. A cellular automata traffic flow model considering the heterogeneity of acceleration and delay probability

    Science.gov (United States)

    Li, Qi-Lang; Wong, S. C.; Min, Jie; Tian, Shuo; Wang, Bing-Hong

    2016-08-01

    This study examines the cellular automata traffic flow model, which considers the heterogeneity of vehicle acceleration and the delay probability of vehicles. Computer simulations are used to identify three typical phases in the model: free-flow, synchronized flow, and wide moving traffic jam. In the synchronized flow region of the fundamental diagram, the low and high velocity vehicles compete with each other and play an important role in the evolution of the system. The analysis shows that there are two types of bistable phases. However, in the original Nagel and Schreckenberg cellular automata traffic model, there are only two kinds of traffic conditions, namely, free-flow and traffic jams. The synchronized flow phase and bistable phase have not been found.

  17. An Extended Cellular Automaton Model for Train Traffic Flow on the Dedicated Passenger Lines

    Directory of Open Access Journals (Sweden)

    Wenbo Zhao

    2014-01-01

    Full Text Available As one of the key components for the railway transportation system, the Train Operation Diagram can be greatly influenced by many extrinsic and intrinsic factors. Therefore, the railway train flow has shown the strong nonlinear characteristics, which makes it quite difficult to take further relative studies. Fortunately, the cellular automaton model has its own advantages in solving nonlinear problems and traffic flow simulation. Considering the mixed features of multispeed running trains on the passenger dedicated lines, this paper presents a new train model under the moving block system with different types of trains running with the cellular automaton idea. By analyzing such key factors as the maintenance skylight, the proportion of the multispeed running trains, and the distance between adjacent stations and departure intervals, the corresponding running rules for the cellular automaton model are reestablished herewith. By means of this CA model, the program of train running system is designed to analyze the potential impact on railway carrying capacity by various factors; the model can also be implemented to simulate the actual train running process and to draw the train operation diagram by computers. Basically the theory can be applied to organize the train operation on the dedicated passenger lines.

  18. In Silico Modeling of the Immune System: Cellular and Molecular Scale Approaches

    Directory of Open Access Journals (Sweden)

    Mariagrazia Belfiore

    2014-01-01

    Full Text Available The revolutions in biotechnology and information technology have produced clinical data, which complement biological data. These data enable detailed descriptions of various healthy and diseased states and responses to therapies. For the investigation of the physiology and pathology of the immune responses, computer and mathematical models have been used in the last decades, enabling the representation of biological processes. In this modeling effort, a major issue is represented by the communication between models that work at cellular and molecular level, that is, multiscale representation. Here we sketch some attempts to model immune system dynamics at both levels.

  19. A Stochastic Cellular Automaton Model of Non-linear Diffusion and Diffusion with Reaction

    Science.gov (United States)

    Brieger, Leesa M.; Bonomi, Ernesto

    1991-06-01

    This article presents a stochastic cellular automaton model of diffusion and diffusion with reaction. The master equations for the model are examined, and we assess the difference between the implementation in which a single particle at a time moves (asynchronous dynamics) and one implementation in which all particles move simultaneously (synchronous dynamics). Biasing locally each particle's random walk, we alter the diffusion coefficients of the system. By appropriately choosing the biasing function, we can impose a desired non-linear diffusive behaviour in the model. We present an application of this model, adapted to include two diffusing species, two static species, and a chemical reaction in a prototypical simulation of carbonation in concrete.

  20. Development and Evaluation of a Cellular Automata Model for Simulating Tillage Erosion in the Presence of Obstacles

    Science.gov (United States)

    Vanwalleghem, T.; Jiménez-Hornero, F. J.; Giráldez, J. V.; Laguna, A.

    2009-04-01

    The process of tillage translocation is well studied and can be described adequately by different existing models. Nevertheless, in complex environments such as olive orchards, characterized by numerous obstacles, application of such conventional tillage erosion models is not straightforward. However, these obstacles have important effects on the spatial pattern of soil redistribution and on resulting soil properties. In this kind of environment, cellular automata could provide a valuable alternative. This study aims at developing a cellular automata model for tillage translocation (CATT) that can take into account such obstacles and at exploring its possibilities and limitations. A simple model was developed, which main parameters are tillage direction, speed and depth. Firstly, the modeĺs outcome was tested against existing 137Cs inventories for a study site in the Belgian loam belt. The observed spatial soil redistribution patterns could be adequately represented by the CATT model. Secondly, a sensitivity analysis was performed to explore the effect of input uncertainty on several selected model outputs. The variance-based extended FAST method was used to determine first and total order sensitivity indices. Tillage depth was identified as the input parameter that determined most of the output variance, followed respectively by tillage direction and speed. The difference between the total and first-order sensitivity indices, between 0.8 and 2, indicated that, in spite of the simple model structure, the model behaves non-linearly with respect to some of the model output variables. Higher-order interactions were especially important for determining the proportion of eroding and deposition cells. Finally, simulations were performed to analyse the model behaviour in complex landscapes, applying it to a field with protruding obstacles (e.g. olive trees). The model adequately represented some morphological features observed in the olive orchards, such as mounds around

  1. Alteration of cellular lipids and lipid metabolism markers in RTL-W1 cells exposed to model endocrine disrupters.

    Science.gov (United States)

    Dimastrogiovanni, Giorgio; Córdoba, Marlon; Navarro, Isabel; Jáuregui, Olga; Porte, Cinta

    2015-08-01

    This work investigates the suitability of the rainbow trout liver cell line (RTL-W1) as an in-vitro model to study the ability of model endocrine disrupters, namely TBT, TPT, 4-NP, BPA and DEHP, to act as metabolic disrupters by altering cellular lipids and markers of lipid metabolism. Among the tested compounds, BPA and DEHP significantly increased the intracellular accumulation of triacylglycerols (TAGs), while all the compounds -apart from TPT-, altered membrane lipids - phosphatidylcholines (PCs) and plasmalogen PCs - indicating a strong interaction of the toxicants with cell membranes and cell signaling. RTL-W1 expressed a number of genes involved in lipid metabolism that were modulated by exposure to BPA, TBT and TPT (up-regulation of FATP1 and FAS) and 4-NP and DEHP (down-regulation of FAS and LPL). Multiple and complex modes of action of these chemicals were observed in RTL-W1 cells, both in terms of expression of genes related to lipid metabolism and alteration of cellular lipids. Although further characterization is needed, this might be a useful model for the detection of chemicals leading to steatosis or other diseases associated with lipid metabolism in fish. PMID:26143618

  2. Interaction between the human cytomegalovirus‑encoded UL142 and cellular Snapin proteins.

    Science.gov (United States)

    Liu, Chang; Qi, Ying; Ma, Yanping; He, Rong; Sun, Zhengrong; Huang, Yujing; Ji, Yaohua; Ruan, Qiang

    2015-02-01

    Human cytomegalovirus (HCMV) infection can cause severe illness in immunocompromised and immunodeficient individuals. As a novel HCMV‑encoded major histocompatibility complex class I‑related molecule, the UL142‑encoded protein (pUL142) is capable of suppressing natural killer (NK) cell recognition in the course of infection. However, no host factors that directly interact with HCMV pUL142 have been reported so far. In order to understand the interactions between HCMV pUL142 and host proteins, the current study used yeast two‑hybrid screening, a GST pull‑down assay and an immunofluorescence assay. A host protein, the SNARE‑associated protein Snapin, was identified to directly interact and colocalize with HCMV pUL142 in transfected human embryonic kidney‑293 cells. Snapin is abundantly expressed in the majority of cells and mediates the release of neurotransmitters through vesicular transport in the nervous system and vesicle fusion in non‑neuronal cells. It is hypothesized that HCMV pUL142 may have an impact on the neurotransmitter release process and viral dissemination via interaction with Snapin. PMID:25369979

  3. Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

    Science.gov (United States)

    Watanabe, Leandro; Myers, Chris J

    2016-08-19

    The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime. PMID:26912276

  4. Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes.

    Directory of Open Access Journals (Sweden)

    Greta E Weiss

    2015-02-01

    Full Text Available During blood stage Plasmodium falciparum infection, merozoites invade uninfected erythrocytes via a complex, multistep process involving a series of distinct receptor-ligand binding events. Understanding each element in this process increases the potential to block the parasite's life cycle via drugs or vaccines. To investigate specific receptor-ligand interactions, they were systematically blocked using a combination of genetic deletion, enzymatic receptor cleavage and inhibition of binding via antibodies, peptides and small molecules, and the resulting temporal changes in invasion and morphological effects on erythrocytes were filmed using live cell imaging. Analysis of the videos have shown receptor-ligand interactions occur in the following sequence with the following cellular morphologies; 1 an early heparin-blockable interaction which weakly deforms the erythrocyte, 2 EBA and PfRh ligands which strongly deform the erythrocyte, a process dependant on the merozoite's actin-myosin motor, 3 a PfRh5-basigin binding step which results in a pore or opening between parasite and host through which it appears small molecules and possibly invasion components can flow and 4 an AMA1-RON2 interaction that mediates tight junction formation, which acts as an anchor point for internalization. In addition to enhancing general knowledge of apicomplexan biology, this work provides a rational basis to combine sequentially acting merozoite vaccine candidates in a single multi-receptor-blocking vaccine.

  5. ModelWizard: Toward Interactive Model Construction

    OpenAIRE

    Hutchison, Dylan

    2016-01-01

    Data scientists engage in model construction to discover machine learning models that well explain a dataset, in terms of predictiveness, understandability and generalization across domains. Questions such as "what if we model common cause Z" and "what if Y's dependence on X reverses" inspire many candidate models to consider and compare, yet current tools emphasize constructing a final model all at once. To more naturally reflect exploration when debating numerous models, we propose an inter...

  6. Interaction of heavy ions with nuclear chromatin: Spatiotemporal investigations of biological responses in a cellular environment

    International Nuclear Information System (INIS)

    Ion beams offer the possibility to generate strictly localized DNA lesions within subregions of a cell nucleus. The distribution of the ion-induced damage can be indirectly visualized by immunocytochemical detection of repair-related proteins as radiation-induced foci. The proteins analyzed here were the double-strand break marker γ-H2AX, the excision repair and replication protein PCNA and the cell cycle regulator CDKN1A. A newly developed adjustable sample holder is now used to apply an irradiation geometry characterized by a small angle between the plane of the cellular monolayer and the incoming ion beam. This allows the spatial analysis of protein accumulations along ion trajectories, revealing an unexpected clustering after irradiation with low-energy zinc ions. The patterns of protein aggregation observed show considerable intrinsic variability, but similar patterns of protein clustering were obtained for functionally different proteins irrespective of the type of ion beam applied, confirming previous observations for lower and higher LET beams. Foci sizes within ion tracks were found to be larger for γ-H2AX foci in comparison to CDKN1A foci, in agreement with the known histone H2AX phosphorylation response. The results suggest that not the pattern of dose deposition but the underlying chromatin structure determines the distribution of protein clusters along tracks. Therefore, the requirement of time-lapse studies using live cells is emphasized for future studies on chromatin movement as a potential component of the DNA damage response

  7. Characterization of the Interaction of Lassa Fever Virus with Its Cellular Receptor α-Dystroglycan

    Science.gov (United States)

    Kunz, Stefan; Rojek, Jillian M.; Perez, Mar; Spiropoulou, Christina F.; Oldstone, Michael B. A.

    2005-01-01

    The cellular receptor for the Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) has recently been identified as α-dystroglycan (α-DG), a cell surface receptor that provides a molecular link between the extracellular matrix and the actin-based cytoskeleton. In the present study, we show that LFV binds to α-DG with high affinity in the low-nanomolar range. Recombinant vesicular stomatitis virus pseudotyped with LFV glycoprotein (GP) adopted the receptor binding characteristics of LFV and depended on α-DG for infection of cells. Mapping of the binding site of LFV on α-DG revealed that LFV binding required the same domains of α-DG that are involved in the binding of LCMV. Further, LFV was found to efficiently compete with laminin α1 and α2 chains for α-DG binding. Together with our previous studies on receptor binding of the prototypic immunosuppressive LCMV isolate LCMV clone 13, these findings indicate a high degree of conservation in the receptor binding characteristics between the highly human-pathogenic LFV and murine-immunosuppressive LCMV isolates. PMID:15857984

  8. Characterization of the interaction of lassa fever virus with its cellular receptor alpha-dystroglycan.

    Science.gov (United States)

    Kunz, Stefan; Rojek, Jillian M; Perez, Mar; Spiropoulou, Christina F; Oldstone, Michael B A

    2005-05-01

    The cellular receptor for the Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) has recently been identified as alpha-dystroglycan (alpha-DG), a cell surface receptor that provides a molecular link between the extracellular matrix and the actin-based cytoskeleton. In the present study, we show that LFV binds to alpha-DG with high affinity in the low-nanomolar range. Recombinant vesicular stomatitis virus pseudotyped with LFV glycoprotein (GP) adopted the receptor binding characteristics of LFV and depended on alpha-DG for infection of cells. Mapping of the binding site of LFV on alpha-DG revealed that LFV binding required the same domains of alpha-DG that are involved in the binding of LCMV. Further, LFV was found to efficiently compete with laminin alpha1 and alpha2 chains for alpha-DG binding. Together with our previous studies on receptor binding of the prototypic immunosuppressive LCMV isolate LCMV clone 13, these findings indicate a high degree of conservation in the receptor binding characteristics between the highly human-pathogenic LFV and murine-immunosuppressive LCMV isolates. PMID:15857984

  9. Nutrient-Gene Interaction in Colon Cancer, from the Membrane to Cellular Physiology.

    Science.gov (United States)

    Hou, Tim Y; Davidson, Laurie A; Kim, Eunjoo; Fan, Yang-Yi; Fuentes, Natividad R; Triff, Karen; Chapkin, Robert S

    2016-07-17

    The International Agency for Research on Cancer recently released an assessment classifying red and processed meat as "carcinogenic to humans" on the basis of the positive association between increased consumption and risk for colorectal cancer. Diet, however, can also decrease the risk for colorectal cancer and be used as a chemopreventive strategy. Bioactive dietary molecules, such as n-3 polyunsaturated fatty acids, curcumin, and fermentable fiber, have been proposed to exert chemoprotective effects, and their molecular mechanisms have been the focus of research in the dietary/chemoprevention field. Using these bioactives as examples, this review surveys the proposed mechanisms by which they exert their effects, from the nucleus to the cellular membrane. In addition, we discuss emerging technologies involving the culturing of colonic organoids to study the physiological effects of dietary bioactives. Finally, we address future challenges to the field regarding the identification of additional molecular mechanisms and other bioactive dietary molecules that can be utilized in our fight to reduce the incidence of colorectal cancer. PMID:27431370

  10. A Geometrical-Based Model for Cochannel Interference Analysis and Capacity Estimation of CDMA Cellular Systems

    Directory of Open Access Journals (Sweden)

    Konstantinos B. Baltzis

    2008-10-01

    Full Text Available A common assumption in cellular communications is the circular-cell approximation. In this paper, an alternative analysis based on the hexagonal shape of the cells is presented. A geometrical-based stochastic model is proposed to describe the angle of arrival of the interfering signals in the reverse link of a cellular system. Explicit closed form expressions are derived, and simulations performed exhibit the characteristics and validate the accuracy of the proposed model. Applications in the capacity estimation of WCDMA cellular networks are presented. Dependence of system capacity of the sectorization of the cells and the base station antenna radiation pattern is explored. Comparisons with data in literature validate the accuracy of the proposed model. The degree of error of the hexagonal and the circular-cell approaches has been investigated indicating the validity of the proposed model. Results have also shown that, in many cases, the two approaches give similar results when the radius of the circle equals to the hexagon inradius. A brief discussion on how the proposed technique may be applied to broadband access networks is finally made.

  11. Antiproliferative Activity and Cellular Uptake of Evodiamine and Rutaecarpine Based on 3D Tumor Models

    Directory of Open Access Journals (Sweden)

    Hui Guo

    2016-07-01

    Full Text Available Evodiamine (EVO and rutaecarpine (RUT are promising anti-tumor drug candidates. The evaluation of the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids of cancer cells would better recapitulate the native situation and thus better reflect an in vivo response to the treatment. Herein, we employed the 3D culture of MCF-7 and SMMC-7721 cells based on hanging drop method and evaluated the anti-proliferative activity and cellular uptake of EVO and RUT in 3D multicellular spheroids, and compared the results with those obtained from 2D monolayers. The drugs’ IC50 values were significantly increased from the range of 6.4–44.1 μM in 2D monolayers to 21.8–138.0 μM in 3D multicellular spheroids, which may be due to enhanced mass barrier and reduced drug penetration in 3D models. The fluorescence of EVO and RUT was measured via fluorescence spectroscopy and the cellular uptake of both drugs was characterized in 2D tumor models. The results showed that the cellular uptake concentrations of RUT increased with increasing drug concentrations. However, the EVO concentrations uptaken by the cells showed only a small change with increasing drug concentrations, which may be due to the different solubility of EVO and Rut in solvents. Overall, this study provided a new vision of the anti-tumor activity of EVO and RUT via 3D multicellular spheroids and cellular uptake through the fluorescence of compounds.

  12. Analysis on Traffic Conflicts of Two-lane Highway Based on Improved Cellular Automation Model

    Directory of Open Access Journals (Sweden)

    Xiru Tang

    2013-06-01

    Full Text Available Based on microscopic traffic characteristics of two-lane highway and different driving characteristics for drivers, the characteristics of drivers and vehicle structure are introduced into Cellular Automation model for establishing new Cellular Automation model of two-lane highway. Through computer simulation, the paper analyzes the effect of the promotion of different vehicles, drivers and arrival rates on traffic conflicts of two-lane highway, which gets the relationship between the parameters such as road traffic and velocity variance and collision. The results indicate that the frequency of traffic conflicts has close relationship with the product of traffic flow and velocity variation. When the traffic flow and velocity variation are great, the frequency of the conflict is the greatest, and when the traffic flow and velocity variation are little, the frequency of the conflict is the least.

  13. Interactions of HIV-1 proteins with their cellular partners : insights from computational methods

    OpenAIRE

    Quy, Vo Cam

    2013-01-01

    HIV-1 attacks vital cells in the human immune system. HIV-1 differs from many viruses since it is characterized by a very high genetic variability. This means that many variants of HIV-1 virus can be generated in a single infected patient in the course of one day. HIV-1 hypervariability causes drug resistance and, consequently, medical treatment failure. Targeting the interactions between proteins from HIV-1 and from Homo sapiens may represent an excellent solution for drug design because it ...

  14. Spatial interactions in agent-based modeling

    CERN Document Server

    Ausloos, Marcel; Merlone, Ugo

    2014-01-01

    Agent Based Modeling (ABM) has become a widespread approach to model complex interactions. In this chapter after briefly summarizing some features of ABM the different approaches in modeling spatial interactions are discussed. It is stressed that agents can interact either indirectly through a shared environment and/or directly with each other. In such an approach, higher-order variables such as commodity prices, population dynamics or even institutions, are not exogenously specified but instead are seen as the results of interactions. It is highlighted in the chapter that the understanding of patterns emerging from such spatial interaction between agents is a key problem as much as their description through analytical or simulation means. The chapter reviews different approaches for modeling agents' behavior, taking into account either explicit spatial (lattice based) structures or networks. Some emphasis is placed on recent ABM as applied to the description of the dynamics of the geographical distribution o...

  15. Computational modeling of laser-tissue interaction

    Energy Technology Data Exchange (ETDEWEB)

    London, R.A.; Amendt, P.; Bailey, D.S.; Eder, D.C.; Maitland, D.J.; Glinsky, M.E.; Strauss, M.; Zimmerman, G.B.

    1996-05-01

    Computational modeling can play an important role both in designing laser-tissue interaction experiments and in understanding the underlying mechanisms. This can lead to more rapid and less expensive development if new procedures and instruments, and a better understanding of their operation. We have recently directed computer programs and associated expertise developed over many years to model high intensity laser-matter interactions for fusion research towards laser-tissue interaction problem. A program called LATIS is being developed to specifically treat laser-tissue interaction phenomena, such as highly scattering light transport, thermal coagulation, and hydrodynamic motion.

  16. A Cascading Failure Model by Quantifying Interactions

    OpenAIRE

    Qi, Junjian; Mei, Shengwei

    2013-01-01

    Cascading failures triggered by trivial initial events are encountered in many complex systems. It is the interaction and coupling between components of the system that causes cascading failures. We propose a simple model to simulate cascading failure by using the matrix that determines how components interact with each other. A careful comparison is made between the original cascades and the simulated cascades by the proposed model. It is seen that the model can capture general features of t...

  17. Numerical simulations for tumor and cellular immune system interactions in lung cancer treatment

    Science.gov (United States)

    Kolev, M.; Nawrocki, S.; Zubik-Kowal, B.

    2013-06-01

    We investigate a new mathematical model that describes lung cancer regression in patients treated by chemotherapy and radiotherapy. The model is composed of nonlinear integro-differential equations derived from the so-called kinetic theory for active particles and a new sink function is investigated according to clinical data from carcinoma planoepitheliale. The model equations are solved numerically and the data are utilized in order to find their unknown parameters. The results of the numerical experiments show a good correlation between the predicted and clinical data and illustrate that the mathematical model has potential to describe lung cancer regression.

  18. Bit-Vectorized GPU Implementation of a Stochastic Cellular Automaton Model for Surface Growth

    CERN Document Server

    Kelling, Jeffrey; Gemming, Sibylle

    2016-01-01

    Stochastic surface growth models aid in studying properties of universality classes like the Kardar--Paris--Zhang class. High precision results obtained from large scale computational studies can be transferred to many physical systems. Many properties, such as roughening and some two-time functions can be studied using stochastic cellular automaton (SCA) variants of stochastic models. Here we present a highly efficient SCA implementation of a surface growth model capable of simulating billions of lattice sites on a single GPU. We also provide insight into cases requiring arbitrary random probabilities which are not accessible through bit-vectorization.

  19. Transfer-matrix DMRG for stochastic models: The Domany-Kinzel cellular automaton

    OpenAIRE

    Kemper, A.; Schadschneider, A.; Zittartz, J.

    2001-01-01

    We apply the transfer-matrix DMRG (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG o...

  20. An Exact Path-Loss Density Model for Mobiles in a Cellular System

    OpenAIRE

    Abdulla, Mouhamed; Shayan, Yousef R.

    2013-01-01

    In trying to emulate the spatial position of wireless nodes for purpose of analysis, we rely on stochastic simulation. And, it is customary, for mobile systems, to consider a base-station radiation coverage by an ideal cell shape. For cellular analysis, a hexagon contour is always preferred mainly because of its tessellating nature. Despite this fact, largely due to its intrinsic simplicity, in literature only random dispersion model for a circular shape is known. However, if considered, this...

  1. A Novel Mathematical Model Describing Adaptive Cellular Drug Metabolism and Toxicity in the Chemoimmune System

    OpenAIRE

    Tóth, Attila; Brózik, Anna; Szakács, Gergely; Sarkadi, Balázs; Hegedüs, Tamás

    2015-01-01

    Cells cope with the threat of xenobiotic stress by activating a complex molecular network that recognizes and eliminates chemically diverse toxic compounds. This “chemoimmune system” consists of cellular Phase I and Phase II metabolic enzymes, Phase 0 and Phase III ATP Binding Cassette (ABC) membrane transporters, and nuclear receptors regulating these components. In order to provide a systems biology characterization of the chemoimmune network, we designed a reaction kinetic model based on d...

  2. Embedding reach-scale fluvial dynamics within the CAESAR cellular automaton landscape evolution model

    Science.gov (United States)

    Van De Wiel, Marco J.; Coulthard, Tom J.; Macklin, Mark G.; Lewin, John

    2007-10-01

    We introduce a new computational model designed to simulate and investigate reach-scale alluvial dynamics within a landscape evolution model. The model is based on the cellular automaton concept, whereby the continued iteration of a series of local process 'rules' governs the behaviour of the entire system. The model is a modified version of the CAESAR landscape evolution model, which applies a suite of physically based rules to simulate the entrainment, transport and deposition of sediments. The CAESAR model has been altered to improve the representation of hydraulic and geomorphic processes in an alluvial environment. In-channel and overbank flow, sediment entrainment and deposition, suspended load and bed load transport, lateral erosion and bank failure have all been represented as local cellular automaton rules. Although these rules are relatively simple and straightforward, their combined and repeatedly iterated effect is such that complex, non-linear geomorphological response can be simulated within the model. Examples of such larger-scale, emergent responses include channel incision and aggradation, terrace formation, channel migration and river meandering, formation of meander cutoffs, and transitions between braided and single-thread channel patterns. In the current study, the model is illustrated on a reach of the River Teifi, near Lampeter, Wales, UK.

  3. Quark models of hadronic interactions

    International Nuclear Information System (INIS)

    The soliton model represents an extension of the MIT bag model to allow for the dynamical degrees of freedom associated with the confinement mechanism. The soliton model has 5 parameters, MIT has 3, but the soliton model has the flexibility, by choice of the parameters, to reproduce either the MIT or the SLAC bags. With appropriate choice of parameters and inclusion of one gluon exchange, the resulting hadronic spectra is similar to the MIT model. Because the model can be cast in Hamiltonian form, dynamical processes can be calculated using techniques developed for nuclear collective motion. This permits calculation of N-N collisions, recoil corrections and the construction of bag states of good momentum. The last is essential for the proper calculation of electromagnetic form factors. In this paper, the pion has been alluded to frequently. It is currently being studied actively in the context of the soliton model. The pion appears here as an anomalously light particle, split off and pushed down from the meson multiplet by OGE. The nucleon bag should be soft to qq, virtual excitation with pion quantum numbers. In the soliton model, these virtual excitations are to be identified with the pion cloud. One can also calculate pi-nucleon coupling and the weak decay of the pion, π → μ + anti nu/sub μ/. Indeed, bags can be created and destroyed in the model. This description of pion physics begins with a Lagrangian which does not respect chiral invariance and seeks to achieve PCAC from dynamics. The more fashionable approach is to begin with a chirally invariant Lagrangian from which the pion emerges as a massless Goldstone boson; somewhere, the pion must be given a mass and CAC broken. In all models, effective fields (sigma or π or both) are introduced to describe degrees of freedom which are too difficult to handle explicitly. 20 references

  4. Modeling of trophospheric ozone concentrations using genetically trained multi-level cellular neural networks

    Science.gov (United States)

    Ozcan, H. Kurtulus; Bilgili, Erdem; Sahin, Ulku; Ucan, O. Nuri; Bayat, Cuma

    2007-09-01

    Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.

  5. Modeling of Trophospheric Ozone Concentrations Using Genetically Trained Multi-Level Cellular Neural Networks

    Institute of Scientific and Technical Information of China (English)

    H. Kurtulus OZCAN; Erdem BILGILI; Ulku SAHIN; O. Nuri UCAN; Cuma BAYAT

    2007-01-01

    Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.

  6. Neutral evolution of Protein-protein interactions: a computational study using simple models

    OpenAIRE

    Simonson Thomas; Noirel Josselin

    2007-01-01

    Abstract Background Protein-protein interactions are central to cellular organization, and must have appeared at an early stage of evolution. To understand better their role, we consider a simple model of protein evolution and determine the effect of an explicit selection for Protein-protein interactions. Results In the model, viable sequences all have the same fitness, following the neutral evolution theory. A very simple, two-dimensional lattice representation of the protein structures is u...

  7. Nanoparticle-allergen interactions mediate human allergic responses: protein corona characterization and cellular responses

    OpenAIRE

    Radauer-Preiml, Isabella; Andosch, Ancuela; Hawranek, Thomas; Luetz-Meindl, Ursula; Wiederstein, Markus; Horejs-Hoeck, Jutta; Himly, Martin; Boyles, Matthew; Duschl, Albert

    2016-01-01

    Background Engineered nanomaterials (ENMs) interact with different biomolecules as soon as they are in contact, resulting in the formation of a biomolecule ‘corona’. Hence, the ‘corona’ defines the biological identity of the ENMs and could affect the response of the immune system to ENM exposure. With up to 40 % of the world population suffering from type I allergy, a possible modulation of allergen effects by binding to ENMs is highly relevant with respect to work place and consumer safety. ...

  8. iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking

    Directory of Open Access Journals (Sweden)

    Yue-Nong Fan

    2014-03-01

    Full Text Available Nuclear receptors (NRs are closely associated with various major diseases such as cancer, diabetes, inflammatory disease, and osteoporosis. Therefore, NRs have become a frequent target for drug development. During the process of developing drugs against these diseases by targeting NRs, we are often facing a problem: Given a NR and chemical compound, can we identify whether they are really in interaction with each other in a cell? To address this problem, a predictor called “iNR-Drug” was developed. In the predictor, the drug compound concerned was formulated by a 256-D (dimensional vector derived from its molecular fingerprint, and the NR by a 500-D vector formed by incorporating its sequential evolution information and physicochemical features into the general form of pseudo amino acid composition, and the prediction engine was operated by the SVM (support vector machine algorithm. Compared with the existing prediction methods in this area, iNR-Drug not only can yield a higher success rate, but is also featured by a user-friendly web-server established at http://www.jci-bioinfo.cn/iNR-Drug/, which is particularly useful for most experimental scientists to obtain their desired data in a timely manner. It is anticipated that the iNR-Drug server may become a useful high throughput tool for both basic research and drug development, and that the current approach may be easily extended to study the interactions of drug with other targets as well.

  9. An improved multi-value cellular automata model for heterogeneous bicycle traffic flow

    International Nuclear Information System (INIS)

    This letter develops an improved multi-value cellular automata model for heterogeneous bicycle traffic flow taking the higher maximum speed of electric bicycles into consideration. The update rules of both regular and electric bicycles are improved, with maximum speeds of two and three cells per second respectively. Numerical simulation results for deterministic and stochastic cases are obtained. The fundamental diagrams and multiple states effects under different model parameters are analyzed and discussed. Field observations were made to calibrate the slowdown probabilities. The results imply that the improved extended Burgers cellular automata (IEBCA) model is more consistent with the field observations than previous models and greatly enhances the realism of the bicycle traffic model. - Highlights: • We proposed an improved multi-value CA model with higher maximum speed. • Update rules are introduced for heterogeneous bicycle traffic with maximum speed 2 and 3 cells/s. • Simulation results of the proposed model are consistent with field bicycle data. • Slowdown probabilities of both regular and electric bicycles are calibrated

  10. An improved multi-value cellular automata model for heterogeneous bicycle traffic flow

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Sheng [College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058 China (China); Qu, Xiaobo [Griffith School of Engineering, Griffith University, Gold Coast, 4222 Australia (Australia); Xu, Cheng [Department of Transportation Management Engineering, Zhejiang Police College, Hangzhou, 310053 China (China); College of Transportation, Jilin University, Changchun, 130022 China (China); Ma, Dongfang, E-mail: mdf2004@zju.edu.cn [Ocean College, Zhejiang University, Hangzhou, 310058 China (China); Wang, Dianhai [College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058 China (China)

    2015-10-16

    This letter develops an improved multi-value cellular automata model for heterogeneous bicycle traffic flow taking the higher maximum speed of electric bicycles into consideration. The update rules of both regular and electric bicycles are improved, with maximum speeds of two and three cells per second respectively. Numerical simulation results for deterministic and stochastic cases are obtained. The fundamental diagrams and multiple states effects under different model parameters are analyzed and discussed. Field observations were made to calibrate the slowdown probabilities. The results imply that the improved extended Burgers cellular automata (IEBCA) model is more consistent with the field observations than previous models and greatly enhances the realism of the bicycle traffic model. - Highlights: • We proposed an improved multi-value CA model with higher maximum speed. • Update rules are introduced for heterogeneous bicycle traffic with maximum speed 2 and 3 cells/s. • Simulation results of the proposed model are consistent with field bicycle data. • Slowdown probabilities of both regular and electric bicycles are calibrated.

  11. Dynamical Models of Dyadic Interactions with Delay

    CERN Document Server

    Bielczyk, Natalia; Płatkowski, Tadeusz

    2012-01-01

    When interpersonal interactions between individuals are described by the (discrete or continuous) dynamical systems, the interactions are usually assumed to be instantaneous: the rates of change of the actual states of the actors at given instant of time are assumed to depend on their states at the same time. In reality the natural time delay should be included in the corresponding models. We investigate a general class of linear models of dyadic interactions with a constant discrete time delay. We prove that in such models the changes of stability of the stationary points from instability to stability or vice versa occur for various intervals of the parameters which determine the intensity of interactions. The conditions guaranteeing arbitrary number (zero, one ore more) of switches are formulated and the relevant theorems are proved. A systematic analysis of all generic cases is carried out. It is obvious that the dynamics of interactions depend both on the strength of reactions of partners on their own sta...

  12. Porous models for wave-seabed interactions

    Energy Technology Data Exchange (ETDEWEB)

    Jeng, Dong-Sheng [Shanghai Jiaotong Univ., SH (China)

    2013-02-01

    Detailed discussion about the phenomenon of wave-seabed interactions. Novel models for wave-induced seabed response. Intensive theoretical derivations for wave-seabed interactions. Practical examples for engineering applications. ''Porous Models for Wave-seabed Interactions'' discusses the Phenomenon of wave-seabed interactions, which is a vital issue for coastal and geotechnical engineers involved in the design of foundations for marine structures such as pipelines, breakwaters, platforms, etc. The most important sections of this book will be the fully detailed theoretical models of wave-seabed interaction problem, which are particularly useful for postgraduate students and junior researchers entering the discipline of marine geotechnics and offshore engineering. This book also converts the research outcomes of theoretical studies to engineering applications that will provide front-line engineers with practical and effective tools in the assessment of seabed instability in engineering design.

  13. Mapping of immunogenic and protein-interacting regions at the surface of the seven-bladed β-propeller domain of the HIV-1 cellular interactor EED

    Directory of Open Access Journals (Sweden)

    Gouet Patrice

    2008-02-01

    Full Text Available Abstract Background The human EED protein, a member of the superfamily of Polycomb group proteins, is involved in multiple cellular protein complexes. Its C-terminal domain, which is common to the four EED isoforms, contains seven repeats of a canonical WD-40 motif. EED is an interactor of three HIV-1 proteins, matrix (MA, integrase (IN and Nef. An antiviral activity has been found to be associated with isoforms EED3 and EED4 at the late stage of HIV-1 replication, due to a negative effect on virus assembly and genomic RNA packaging. The aim of the present study was to determine the regions of the EED C-terminal core domain which were accessible and available to protein interactions, using three-dimensional (3D protein homology modelling with a WD-40 protein of known structure, and epitope mapping of anti-EED antibodies. Results Our data suggested that the C-terminal domain of EED was folded as a seven-bladed β-propeller protein. During the completion of our work, crystallographic data of EED became available from co-crystals of the EED C-terminal core with the N-terminal domain of its cellular partner EZH2. Our 3D-model was in good congruence with the refined structural model determined from crystallographic data, except for a unique α-helix in the fourth β-blade. More importantly, the position of flexible loops and accessible β-strands on the β-propeller was consistent with our mapping of immunogenic epitopes and sites of interaction with HIV-1 MA and IN. Certain immunoreactive regions were found to overlap with the EZH2, MA and IN binding sites, confirming their accessibility and reactivity at the surface of EED. Crystal structure of EED showed that the two discrete regions of interaction with MA and IN did not overlap with each other, nor with the EZH2 binding pocket, but were contiguous, and formed a continuous binding groove running along the lateral face of the β-propeller. Conclusion Identification of antibody-, MA-, IN- and EZH2

  14. Matrix models with Penner interaction inspired by interacting ribonucleic acid

    Indian Academy of Sciences (India)

    Pradeep Bhadola; N Deo

    2015-02-01

    The Penner interaction known in studies of moduli space of punctured Riemann surfaces is introduced and studied in the context of random matrix model of homo RNA. An analytic derivation of the generating function is given and the corresponding partition function is derived numerically. An additional dependence of the structure combinatorics factor on (related to the size of the matrix and the interaction strength) is obtained. This factor has a strong effect on the structure combinatorics in the low regime. Databases are scanned for real ribonucleic acid (RNA) structures and pairing information for these RNA structures is computationally extracted. Then the genus is calculated for every structure and plotted as a function of length. The genus distribution function is compared with the prediction from the nonlinear (NL) model. The specific heat and distribution of structure with temperature calculated from the NL model shows that the NL inter-action is biased towards planar structures. The second derivative of specific heat changes phase from a double peaked function for small to a single peak for large . Detailed analysis reveals the presence of the double peak only for genus 0 structures, the higher genii behave normally with . Comparable behaviour is found in studies involving interactions of RNA with osmolytes and monovalent cations in unfolding experiments.

  15. Modelling land-use effects of future urbanization using cellular automata

    DEFF Research Database (Denmark)

    Fuglsang, Morten; Münier, B.; Hansen, H.S.

    2013-01-01

    The modelling of land use change is a way to analyse future scenarios by modelling different pathways. Application of spatial data of different scales coupled with socio-economic data makes it possible to explore and test the understanding of land use change relations. In the EU-FP7 research...... project PASHMINA (Paradigm Shift modelling and innovative approaches), three storylines of future transportation paradigm shifts towards 2040 are created. These storylines are translated into spatial planning strategies and modelled using the cellular automata model LUCIA. For the modelling, an Eastern...... Danish case area was selected, comprising of the Copenhagen metropolitan area and its hinterland. The different scenarios are described using a range of different descriptive GIS datasets. These include mapping of accessibility based on public and private transportation, urban density and structure, and...

  16. CELLULAR AUTOMATA MODELLING OF GRAIN COARSENING DURING REIHEATING AND VALIDATION WITH THE EXPERIMENTAL RESULTS

    Institute of Scientific and Technical Information of China (English)

    W.H. Yu; E.J. Palmiere; S.P. Banks; J.T. Han

    2005-01-01

    A novel 2D cellular automata (CA) model has been developed for description of normal grain coarsening and abnormal grain coarsening process. The program reflects the grain coarsening quite well even through the average grain size becomes very large. Follow results have been obtained: (a) The model reflect the normal grain growth kinetics gradually increase with probability and grain growth speed can be controlled. Based on this result, temperature can be coupled in the model. (b) Abnormal grain growth is modelled successfully. (c) Methodology has been put forward to find the relationship between the experiment results and modelling results. The experimental work on the grain coarsening has been carried out. Graphical output matched the realistic microstructure in every detail. Because many physical parameters can be taken into account in the CA programme, this CA model could not only qualitatively demonstrate the grain growth process, but also quantitatively predict and analyse the grain coarsening process.

  17. Random walk theory of jamming in a cellular automaton model for traffic flow

    Science.gov (United States)

    Barlovic, Robert; Schadschneider, Andreas; Schreckenberg, Michael

    2001-05-01

    The jamming behavior of a single lane traffic model based on a cellular automaton approach is studied. Our investigations concentrate on the so-called VDR model which is a simple generalization of the well-known Nagel-Schreckenberg model. In the VDR model one finds a separation between a free flow phase and jammed vehicles. This phase separation allows to use random walk like arguments to predict the resolving probabilities and lifetimes of jam clusters or disturbances. These predictions are in good agreement with the results of computer simulations and even become exact for a special case of the model. Our findings allow a deeper insight into the dynamics of wide jams occuring in the model.

  18. Ethanol regulation of adenosine receptor-stimulated cAMP levels in a clonal neural cell line: an in vitro model of cellular tolerance to ethanol.

    OpenAIRE

    Gordon, A S; Collier, K; Diamond, I.

    1986-01-01

    The acute and chronic neurologic effects of ethanol appear to be due to its interaction with neural cell membranes. Chronic exposure to ethanol induces changes in the membrane that lead to tolerance to the effects of ethanol. However, the actual membrane changes that account for tolerance to ethanol are not understood. We have developed a model cell culture system, using NG108-15 neuroblastoma-glioma hybrid cells, to study cellular tolerance to ethanol. We have found that adenosine receptor-s...

  19. Using Interaction Scenarios to Model Information Systems

    DEFF Research Database (Denmark)

    Bækgaard, Lars; Bøgh Andersen, Peter

    The purpose of this paper is to define and discuss a set of interaction primitives that can be used to model the dynamics of socio-technical activity systems, including information systems, in a way that emphasizes structural aspects of the interaction that occurs in such systems. The primitives...

  20. Abstract polymer models with general pair interactions

    CERN Document Server

    Procacci, Aldo

    2007-01-01

    A convergence criterion of cluster expansion is presented in the case of an abstract polymer system with general pair interactions (i.e. not necessarily hard core or repulsive). As a concrete example, the low temperature disordered phase of the BEG model with infinite range interactions, decaying polynomially as $1/r^{d+\\lambda}$ with $\\lambda>0$, is studied.

  1. Cellular and biophysical evidence for interactions between adenosine triphosphate and P-glycoprotein substrates

    DEFF Research Database (Denmark)

    Abraham, E H; Shrivastav, B; Salikhova, A Y;

    2001-01-01

    P-glycoprotein is involved with the removal of drugs, most of them cations, from the plasma membrane and cytoplasm. Pgp is also associated with movement of ATP, an anion, from the cytoplasm to the extracellular space. The central question of this study is whether drug and ATP transport associated...... with the expression of Pgp are in any way coupled. We have measured the stoichiometry of transport coupling between drug and ATP release. The drug and ATP transport that is inhibitable by the sulfonylurea compound, glyburide (P. E. Golstein, A. Boom, J. van Geffel, P. Jacobs, B. Masereel, and R....... Beauwens, Pfluger's Arch. 437, 652, 1999), permits determination of the transport coupling ratio, which is close to 1:1. In view of this result, we asked whether ATP interacts directly with Pgp substrates. We show by measuring the movement of Pgp substrates in electric fields that ATP and drug movement are...

  2. Suppression of cellular transformation by poly (A binding protein interacting protein 2 (Paip2.

    Directory of Open Access Journals (Sweden)

    Amy B Rosenfeld

    Full Text Available Controlling translation is crucial for the homeostasis of a cell. Its deregulation can facilitate the development and progression of many diseases including cancer. Poly (A binding protein interacting protein 2 (Paip2 inhibits efficient initiation of translation by impairing formation of the necessary closed loop of mRNA. The over production of Paip2 in the presence of a constitutively active form of hRas(V12 can reduce colony formation in a semi-solid matrix and focus formation on a cell monolayer. The ability of Paip2 to bind to Pabp is required to suppress the transformed phenotype mediated by hRas(V12. These observations indicate that Paip2 is able to function as a tumor suppressor.

  3. Interacting Induced Dark Energy Model

    OpenAIRE

    Bahrehbakhsh, Amir F.

    2016-01-01

    Similar to the idea of the brane world scenarios, but based on the approach of the induced matter theory, for a non--vacuum five--dimensional version of general relativity, we propose a model in which the conventional matter sources considered as all kind of the matter (the baryonic and dark) and the induced terms emerging from the extra dimension supposed to be as dark energy. Then we investigate the FLRW type cosmological equations and illustrate that the model is capable to explain respect...

  4. Mechanism of Laser/light beam interaction at cellular and tissue level and study of the influential factors for the application of low level laser therapy

    OpenAIRE

    Khalid, Muhammad Zeeshan

    2016-01-01

    After the discovery of laser therapy it was realized it has useful application of wound healing and reduce pain, but due to the poor understanding of the mechanism and dose response this technique remained to be controversial for therapeutic applications. In order to understand the working and effectiveness different experiments were performed to determine the laser beam effect at the cellular and tissue level. This article discusses the mechanism of beam interaction at tissues and cellular l...

  5. Interaction of the Papillomavirus E8∧E2C Protein with the Cellular CHD6 Protein Contributes to Transcriptional Repression▿ †

    OpenAIRE

    Fertey, Jasmin; Ammermann, Ingo; Winkler, Michael; Stöger, Reinhard; Iftner, Thomas; Stubenrauch, Frank

    2010-01-01

    Expression of the E6 and E7 oncogenes of high-risk human papillomaviruses (HPV) is controlled by cellular transcription factors and by viral E2 and E8∧E2C proteins, which are both derived from the HPV E2 gene. Both proteins bind to and repress the HPV E6/E7 promoter. Promoter inhibition has been suggested to be due to binding site competition with cellular transcription factors and to interactions of different cellular transcription modulators with the different amino termini of E2 and E8∧E2C...

  6. A Cellular Automaton Model for Heterogeneous and Incosistent Driver Behavior in Urban Traffic

    Science.gov (United States)

    Liu, Ming-Zhe; Zhao, Shi-Bo; Wang, Rui-Li

    2012-11-01

    In this paper a cellular automaton model is proposed to describe driver behavior at a single-lane urban roundabout. Driver behavior has been considered as heterogeneous and inconsistent. Most traffic papers in the literature just discussed heterogeneous driver behavior, to our best knowledge. Two truncated Gaussian distributions are used to model heterogeneous and inconsistent driver behavior, respectively. The physical meanings of two truncated distributions are indicated. This method may help enhance a better understanding of driver behavior at roundabout traffic, and even possibly provide references for roundabout design and management.

  7. A Cellular Automaton Model for Heterogeneous and Incosistent Driver Behavior in Urban Traffic

    Institute of Scientific and Technical Information of China (English)

    LIUMing-Zhe; ZHAO Shi-Bo; WANG Rui-Li

    2012-01-01

    In this paper a cellular automaton model is proposed to describe driver behavior at a single-lane urban roundabout. Driver behavior has been considered as heterogeneous and inconsistent. Most traffic papers in the literature just discussed heterogeneous driver behavior, to our best knowledge. Two truncated Caussian distributions are used to model heterogeneous and inconsistent driver behavior, respectively. The physical meanings of two truncated distributions are indicated. This method may help enhance a better understanding of driver behavior at roundabout traffic, and even possibly provide references for roundabout design and management.

  8. Interaction Spline Models and Their Convergence Rates

    OpenAIRE

    Chen, Zehua

    1991-01-01

    We consider interaction splines which model a multivariate regression function $f$ as a constant plus the sum of functions of one variable (main effects), plus the sum of functions of two variables (two-factor interactions), and so on. The estimation of $f$ by the penalized least squares method and the asymptotic properties of the models are studied in this article. It is shown that, under some regularity conditions on the data points, the expected squared error averaged over the data points ...

  9. Functional Modeling of Neural-Glia Interaction

    DEFF Research Database (Denmark)

    Postnov, D.E.; Brazhe, N.A.; Sosnovtseva, Olga

    2012-01-01

    Functional modeling is an approach that focuses on the representation of the qualitative dynamics of the individual components (e.g. cells) of a system and on the structure of the interaction network.......Functional modeling is an approach that focuses on the representation of the qualitative dynamics of the individual components (e.g. cells) of a system and on the structure of the interaction network....

  10. A Heuristic Molecular Model of Hydrophobic Interactions

    OpenAIRE

    Hummer, G.; Garde, S.; Garcia, A. E.; Pohorille, A.; Pratt, L. R.

    1995-01-01

    Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics...

  11. Advances in modeling of biomolecular interactions

    Institute of Scientific and Technical Information of China (English)

    Cong-zhongCAI; Ze-rongLI; Wan-luWANG; Yu-zongCHEN

    2004-01-01

    Modeling of molecular interactions is increasingly used in life science research and biotechnology development.Examples are computer aided drug design, prediction of protein interactions with other molecules, and simulation of networks of biomolecules in a particular process in human body. This article reviews recent progress in the related fields and provides a brief overview on the methods used in molecular modeling of biological systems.

  12. Numerical modeling of magma-repository interactions

    OpenAIRE

    Bokhove, O.

    2001-01-01

    This report explains the numerical programs behind a comprehensive modeling effort of magma-repository interactions. Magma-repository interactions occur when a magma dike with high-volatile content magma ascends through surrounding rock and encounters a tunnel or drift filled with either a magmatic gas or air at atmospheric pressure. The simplified mathematical model to describe these flow phenomena consists of compressible flow equations of one- or two-dimensional flow in a flow tube with a ...

  13. Modeling Mixed Bicycle Traffic Flow: A Comparative Study on the Cellular Automata Approach

    Directory of Open Access Journals (Sweden)

    Dan Zhou

    2015-01-01

    Full Text Available Simulation, as a powerful tool for evaluating transportation systems, has been widely used in transportation planning, management, and operations. Most of the simulation models are focused on motorized vehicles, and the modeling of nonmotorized vehicles is ignored. The cellular automata (CA model is a very important simulation approach and is widely used for motorized vehicle traffic. The Nagel-Schreckenberg (NS CA model and the multivalue CA (M-CA model are two categories of CA model that have been used in previous studies on bicycle traffic flow. This paper improves on these two CA models and also compares their characteristics. It introduces a two-lane NS CA model and M-CA model for both regular bicycles (RBs and electric bicycles (EBs. In the research for this paper, many cases, featuring different values for the slowing down probability, lane-changing probability, and proportion of EBs, were simulated, while the fundamental diagrams and capacities of the proposed models were analyzed and compared between the two models. Field data were collected for the evaluation of the two models. The results show that the M-CA model exhibits more stable performance than the two-lane NS model and provides results that are closer to real bicycle traffic.

  14. Biomechanics and Thermodynamics of Nanoparticle Interactions with Plasma and Endosomal Membrane Lipids in Cellular Uptake and Endosomal Escape

    OpenAIRE

    Peetla, Chiranjeevi; Jin, Shihua; Weimer, Jonathan; Elegbede, Adekunle; Labhasetwar, Vinod

    2014-01-01

    To be effective for cytoplasmic delivery of therapeutics, nanoparticles (NPs) taken up via endocytic pathways must efficiently transport across the cell membrane and subsequently escape from the secondary endosomes. We hypothesized that the biomechanical and thermodynamic interactions of NPs with plasma and endosomal membrane lipids are involved in these processes. Using model plasma and endosomal lipid membranes, we compared the interactions of cationic NPs composed of poly(d,l-lactide-co-gl...

  15. Modeling presynapse-astrocyte interactions

    OpenAIRE

    Kerstin Lenk

    2015-01-01

    Astrocytes have gained an increased interest in neuroscience due to their ability to influence synaptic transmission through gliotransmitters. Many studies and models concentrate on tripartite synapses formed by two neurons and an astrocyte. The effects of tripartite synapse on paired pulse facilitation and depression were suggested for example by De Pittá et al. (PLoS Comput. Biol. 2011). In the presented work we concentrated on the pathway from the presynapse to the astrocyte and back to th...

  16. Syndetic model of fundamental interactions

    Directory of Open Access Journals (Sweden)

    Ernest Ma

    2015-02-01

    Full Text Available The standard model of quarks and leptons is extended to connect three outstanding issues in particle physics and astrophysics: (1 the absence of strong CP nonconservation, (2 the existence of dark matter, and (3 the mechanism of nonzero neutrino masses, and that of the first family of quarks and leptons, all in the context of having only one Higgs boson in a renormalizable theory. Some phenomenological implications are discussed.

  17. Instructional systems development model for interactive videodisc

    Science.gov (United States)

    Campbell, J. O.; Tuttle, D. M.; Gibbons, A. S.

    1983-12-01

    This is the third and final report on an Instructional Systems Development Model for Videodisc Training Delivery Systems with Interactive Capability. The report reviews the current state of the art, and describes two videodiscs made for the project, with lessons learned from them. Each block of the Interservice Procedures for Instructional Systems Development (IPISD) is described in terms of the new opportunities and requirements of interactive videodisc. A separate report, "Interactive Videodisc Design and Production Workshop Guide,' presents a step by step procedure for making interactive videodiscs.

  18. On the Photonic Cellular Interaction and the Electric Activity of Neurons in the Human Brain

    International Nuclear Information System (INIS)

    The subject of Ultraweak Photon Emission (UPE) by biological systems is very fascinating, and both evidence of its effects and applications are growing rapidly due to improvements in experimental techniques. Since the relevant equipment should be ultrasensitive with high quantum efficiencies and very low noise levels, the subject of UPE is still hotly debated and some of the interpretations need stronger empirical evidence to be accepted at face value. In this paper we first review different types of interactions between light and living systems based on recent publications. We then discuss the feasibility of UPE production in the human brain. The subject of UPE in the brain is still in early stages of development and needs more accurate experimental methods for proper analysis. In this work we also discuss a possible role of mitochondria in the production of UPE in the neurons of the brain and the plausibility of their effects on microtubules (MTs). MTs have been implicated as playing an important role in the signal and information processing taking place in the mammalian (especially human) brain. Finally, we provide a short discussion about the feasible effects of MTs on electric neural activity in the human brain.

  19. 2D cellular automaton model for the evolution of active region coronal plasmas

    CERN Document Server

    Fuentes, Marcelo López

    2016-01-01

    We study a 2D cellular automaton (CA) model for the evolution of coronal loop plasmas. The model is based on the idea that coronal loops are made of elementary magnetic strands that are tangled and stressed by the displacement of their footpoints by photospheric motions. The magnetic stress accumulated between neighbor strands is released in sudden reconnection events or nanoflares that heat the plasma. We combine the CA model with the Enthalpy Based Thermal Evolution of Loops (EBTEL) model to compute the response of the plasma to the heating events. Using the known response of the XRT telescope on board Hinode we also obtain synthetic data. The model obeys easy to understand scaling laws relating the output (nanoflare energy, temperature, density, intensity) to the input parameters (field strength, strand length, critical misalignment angle). The nanoflares have a power-law distribution with a universal slope of -2.5, independent of the input parameters. The repetition frequency of nanoflares, expressed in t...

  20. Numerical study on photoresist etching processes based on a cellular automata model

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    For the three-dimensional (3-D) numerical study of photoresist etching processes, the 2-D dynamic cellular automata (CA) model has been successfully extended to a 3-D dynamic CA model. Only the boundary cells will be processed in the 3-D dy-namic CA model and the structure of “if-else” description in the simulation pro-gram is avoided to speed up the simulation. The 3-D dynamic CA model has found to be stable, fast and accurate for the numerical study of photoresist etching processes. The exposure simulation, post-exposure bake (PEB) simulation and etching simulation are integrated together to further investigate the performances of the CA model. Simulation results have been compared with the available ex-perimental results and the simulations show good agreement with the available experiments.

  1. Numerical study on photoresist etching processes based on a cellular automata model

    Institute of Scientific and Technical Information of China (English)

    ZHOU ZaiFa; HUANG QingAn; LI WeiHua; LU Wei

    2007-01-01

    For the three-dimensional (3-D) numerical study of photoresist etching processes, the 2-D dynamic cellular automata (CA) model has been successfully extended to a 3-D dynamic CA model. Only the boundary cells will be processed in the 3-D dynamic CA model and the structure of "if-else" description in the simulation program is avoided to speed up the simulation. The 3-D dynamic CA model has found to be stable, fast and accurate for the numerical study of photoresist etching processes. The exposure simulation, post-exposure bake (PEB) simulation and etching simulation are integrated together to further investigate the performances of the CA model. Simulation results have been compared with the available experimental results and the simulations show good agreement with the available experiments.

  2. A traffic flow cellular automaton model to considering drivers' learning and forgetting behaviour

    Institute of Scientific and Technical Information of China (English)

    Ding Jian-Xun; Huang Hai-Jun; Tian Qiong

    2011-01-01

    It is known that the commonly used NaSch cellular automaton (CA) model and its modifications can help explain the internal causes of the macro phenomena of traffic flow. However, the randomization probability of vehicle velocity used in these models is assumed to be an exogenous constant or a conditional constant, which cannot reflect the learning and forgetting behaviour of drivers with historical experiences. This paper further modifies the NaSch model by enabling the randomization probability to be adjusted on the bases of drivers' memory. The Markov properties of this modified model are discussed. Analytical and simulation results show that the traffic fundamental diagrams can be indeed improved when considering drivers' intelligent behaviour. Some new features of traffic are revealed by differently combining the model parameters representing learning and forgetting behaviour.

  3. A novel mathematical model describing adaptive cellular drug metabolism and toxicity in the chemoimmune system.

    Directory of Open Access Journals (Sweden)

    Attila Tóth

    Full Text Available Cells cope with the threat of xenobiotic stress by activating a complex molecular network that recognizes and eliminates chemically diverse toxic compounds. This "chemoimmune system" consists of cellular Phase I and Phase II metabolic enzymes, Phase 0 and Phase III ATP Binding Cassette (ABC membrane transporters, and nuclear receptors regulating these components. In order to provide a systems biology characterization of the chemoimmune network, we designed a reaction kinetic model based on differential equations describing Phase 0-III participants and regulatory elements, and characterized cellular fitness to evaluate toxicity. In spite of the simplifications, the model recapitulates changes associated with acquired drug resistance and allows toxicity predictions under variable protein expression and xenobiotic exposure conditions. Our simulations suggest that multidrug ABC transporters at Phase 0 significantly facilitate the defense function of successive network members by lowering intracellular drug concentrations. The model was extended with a novel toxicity framework which opened the possibility of performing in silico cytotoxicity assays. The alterations of the in silico cytotoxicity curves show good agreement with in vitro cell killing experiments. The behavior of the simplified kinetic model suggests that it can serve as a basis for more complex models to efficiently predict xenobiotic and drug metabolism for human medical applications.

  4. Calibrating Cellular Automata of Land Use/cover Change Models Using a Genetic Algorithm

    Science.gov (United States)

    Mas, J. F.; Soares-Filho, B.; Rodrigues, H.

    2015-08-01

    Spatially explicit land use / land cover (LUCC) models aim at simulating the patterns of change on the landscape. In order to simulate landscape structure, the simulation procedures of most computational LUCC models use a cellular automata to replicate the land use / cover patches. Generally, model evaluation is based on assessing the location of the simulated changes in comparison to the true locations but landscapes metrics can also be used to assess landscape structure. As model complexity increases, the need to improve calibration and assessment techniques also increases. In this study, we applied a genetic algorithm tool to optimize cellular automata's parameters to simulate deforestation in a region of the Brazilian Amazon. We found that the genetic algorithm was able to calibrate the model to simulate more realistic landscape in term of connectivity. Results show also that more realistic simulated landscapes are often obtained at the expense of the location coincidence. However, when considering processes such as the fragmentation impacts on biodiversity, the simulation of more realistic landscape structure should be preferred to spatial coincidence performance.

  5. Local Cellular Immune Responses and Pathogenesis of Buruli Ulcer Lesions in the Experimental Mycobacterium Ulcerans Pig Infection Model

    Science.gov (United States)

    Bolz, Miriam; Ruggli, Nicolas; Borel, Nicole; Pluschke, Gerd; Ruf, Marie-Thérèse

    2016-01-01

    Background Buruli ulcer is a neglected tropical disease of the skin that is caused by infection with Mycobacterium ulcerans. We recently established an experimental pig (Sus scrofa) infection model for Buruli ulcer to investigate host-pathogen interactions, the efficacy of candidate vaccines and of new treatment options. Methodology/Principal Findings Here we have used the model to study pathogenesis and early host-pathogen interactions in the affected porcine skin upon infection with mycolactone-producing and non-producing M. ulcerans strains. Histopathological analyses of nodular lesions in the porcine skin revealed that six weeks after infection with wild-type M. ulcerans bacteria extracellular acid fast bacilli were surrounded by distinct layers of neutrophils, macrophages and lymphocytes. Upon ulceration, the necrotic tissue containing the major bacterial burden was sloughing off, leading to the loss of most of the mycobacteria. Compared to wild-type M. ulcerans bacteria, toxin-deficient mutants caused an increased granulomatous cellular infiltration without massive tissue necrosis, and only smaller clusters of acid fast bacilli. Conclusions/Significance In summary, the present study shows that the pathogenesis and early immune response to M. ulcerans infection in the pig is very well reflecting BU disease in humans, making the pig infection model an excellent tool for the profiling of new therapeutic and prophylactic interventions. PMID:27128097

  6. An inhibitory interaction between viral and cellular proteins underlies the resistance of tomato to nonadapted tobamoviruses.

    Science.gov (United States)

    Ishibashi, Kazuhiro; Naito, Satoshi; Meshi, Tetsuo; Ishikawa, Masayuki

    2009-05-26

    Any individual virus can infect only a limited range of hosts, and most plant species are "nonhosts" to a given virus; i.e., all members of the species are insusceptible to the virus. In nonhost plants, the factors that control virus resistance are not genetically tractable, and how the host range of a virus is determined remains poorly understood. Tomato (Solanum lycopersicum) is a nonhost species for Tobacco mild green mosaic virus (TMGMV) and Pepper mild mottle virus (PMMoV), members of the genus Tobamovirus. Previously, we identified Tm-1, a resistance gene of tomato to another tobamovirus, Tomato mosaic virus (ToMV), and found that Tm-1 binds to ToMV replication proteins to inhibit RNA replication. Tm-1 is derived from a wild tomato species, S. habrochaites, and ToMV-susceptible tomato cultivars have the allelic gene tm-1. The tm-1 protein can neither bind to ToMV replication proteins nor inhibit ToMV multiplication. Here, we show that transgenic tobacco plants expressing tm-1 exhibit resistance to TMGMV and PMMoV. The tm-1 protein bound to the replication proteins of TMGMV and PMMoV and inhibited their RNA replication in vitro. In one of the tm-1-expressing tobacco plants, a tm-1-insensitive TMGMV mutant emerged. In tomato protoplasts, this mutant TMGMV multiplied as efficiently as ToMV. However, in tomato plants, the mutant TMGMV multiplied with lower efficiency compared to ToMV and caused systemic necrosis. These results suggest that an inhibitory interaction between the replication proteins and tm-1 underlies a multilayered resistance mechanism to TMGMV in tomato. PMID:19423673

  7. Looking for a needle in a haystack: Cellular proteins that may interact with the tyrosine-based sorting signal of the TGEV S protein.

    Science.gov (United States)

    Trincone, Anna; Schwegmann-Weßels, Christel

    2015-04-16

    The spike protein S of transmissible gastroenteritis virus, an Alphacoronavirus, contains a tyrosine-based sorting signal that is responsible for ERGIC retention and may be important for a correct viral assembly process. To find out whether the S protein interacts with cellular proteins via this sorting signal, a pulldown assay with GST fusion proteins was performed. Filamin A has been identified as a putative interaction candidate. Immunofluorescence assays confirmed a co-localization between the TGEV S protein and filamin A. Further experiments have to be performed to prove a significant impact of filamin A on TGEV infection. Different approaches of several researchers for the identification of cellular interaction candidates relevant for coronavirus replication are summarized. These results may help in the future to identify the role of cellular proteins during coronavirus assembly at the ER-Golgi intermediate compartment. PMID:25481285

  8. A Survey On Interactivity in Topic Models

    Directory of Open Access Journals (Sweden)

    Patrik Ehrencrona Kjellin

    2016-04-01

    Full Text Available Trying to make sense and gain deeper insight from large sets of data is becoming a task very central to computer science in general. Topic models, capable of uncovering the semantic themes pervading through large collections of documents, have seen a surge in popularity in recent years. However, topic models are high level statistical tools; their output is given in terms of probability distributions, suited neither for simple interpretation nor deep analysis. Interpreting the fitted topic models in an intuitive manner requires visual and interactive tools. Additionally, some measure of human interaction is typically required for refining the output offered by such models. In the research, this area remains relatively unexplored – only recently has this aspect been receiving more attention. In this paper, the literature is surveyed as it pertains to interactivity and visualisation within the context of topic models, with the goal of finding current research trends in this area.

  9. Interaction of Streptococcus agalactiae and cellular innate immunity in colonization and disease

    Directory of Open Access Journals (Sweden)

    Sybille eLandwehr-Kenzel

    2014-10-01

    Full Text Available Streptococcus agalactiae (Group B streptococcus, GBS is highly adapted to humans, where it is a normal constituent of the intestinal and vaginal flora. Yet, GBS has highly invasive potential and causes excessive inflammation, sepsis and death at the beginning of life, in the elderly and in diabetic patients. Thus GBS is a model pathobiont that thrives in the healthy host, but has not lost its potential virulence during coevolution with mankind. It remains incompletely understood how the innate immune system contains GBS in the natural niches, the intestinal and genital tracts, and which molecular events underlie breakdown of mucocutaneous resistance. Newborn infants between days seven and 90 of life are at risk of a particularly striking sepsis manifestation (late onset disease, LOD, where the transition from colonization to invasion and dissemination, and thus from health to severe sepsis is typically fulminant and not predictable. The great majority of late-onset sepsis cases is caused by one clone, GBS ST-17, which expresses HvgA as a signature virulence factor and adhesin. In mice, HvgA promotes the crossing of both the mucosal and the blood brain barrier. Expression levels of HvgA and other GBS virulence factors, such as pili and toxins, are regulated by the upstream two-component control system CovR/S. This in turn is modulated by acidic epithelial pH, high glucose levels and during the passage through the mouse intestine. After invasion, GBS has the ability to subvert innate immunity by mechanisms like GAPDH-dependent induction of IL-10 and β-protein binding to the inhibitory phagocyte receptors sialic acid binding immunoglobulin-like lectin 5 and 14. On the host side, sensing of GBS nucleic acids and lipopeptides by both Toll-like receptors (TLRs and the inflammasome appears to be critical for host resistance against GBS. Yet, comprehensive models on the interplay between GBS and human immune cells at the colonizing site are just

  10. A general allometric and life-history model for cellular differentiation in the transition to multicellularity.

    Science.gov (United States)

    Solari, Cristian A; Kessler, John O; Goldstein, Raymond E

    2013-03-01

    The transition from unicellular, to colonial, to larger multicellular organisms has benefits, costs, and requirements. Here we present a model inspired by the volvocine green algae that explains the dynamics involved in the unicellular-multicellular transition using life-history theory and allometry. We model the two fitness components (fecundity and viability) and compare the fitness of hypothetical colonies of different sizes with varying degrees of cellular differentiation to understand the general principles that underlie the evolution of multicellularity. We argue that germ-soma separation may have evolved to counteract the increasing costs and requirements of larger multicellular colonies. The model shows that the cost of investing in soma decreases with size. For lineages such as the Volvocales, as reproduction costs increase with size for undifferentiated colonies, soma specialization benefits the colony indirectly by decreasing such costs and directly by helping reproductive cells acquire resources for their metabolic needs. Germ specialization is favored once soma evolves and takes care of vegetative functions. To illustrate the model, we use some allometric relationships measured in Volvocales. Our analysis shows that the cost of reproducing an increasingly larger group has likely played an important role in the transition to multicellularity and cellular differentiation. PMID:23448886

  11. Simulation of emotional contagion using modified SIR model: A cellular automaton approach

    Science.gov (United States)

    Fu, Libi; Song, Weiguo; Lv, Wei; Lo, Siuming

    2014-07-01

    Emotion plays an important role in the decision-making of individuals in some emergency situations. The contagion of emotion may induce either normal or abnormal consolidated crowd behavior. This paper aims to simulate the dynamics of emotional contagion among crowds by modifying the epidemiological SIR model to a cellular automaton approach. This new cellular automaton model, entitled the “CA-SIRS model”, captures the dynamic process ‘susceptible-infected-recovered-susceptible', which is based on SIRS contagion in epidemiological theory. Moreover, in this new model, the process is integrated with individual movement. The simulation results of this model show that multiple waves and dynamical stability around a mean value will appear during emotion spreading. It was found that the proportion of initial infected individuals had little influence on the final stable proportion of infected population in a given system, and that infection frequency increased with an increase in the average crowd density. Our results further suggest that individual movement accelerates the spread speed of emotion and increases the stable proportion of infected population. Furthermore, decreasing the duration of an infection and the probability of reinfection can markedly reduce the number of infected individuals. It is hoped that this study will be helpful in crowd management and evacuation organization.

  12. Non-linearity and spatial resolution in a cellular automaton model of a small upland basin

    Directory of Open Access Journals (Sweden)

    T. J. Coulthard

    1998-01-01

    Full Text Available The continuing development of computational fluid dynamics is allowing the high resolution study of hydraulic and sediment transport processes but, due to computational complexities, these are rarely applied to areas larger than a reach. Existing approaches, based upon linked cross sections, can give a quasi two-dimensional view, effectively simulating sediment transport for a single river reach. However, a basin represents a whole discrete dynamic system within which channel, floodplain and slope processes operate over a wide range of space and time scales. Here, a cellular automaton (CA approach has been used to overcome some of these difficulties, in which the landscape is represented as a series of fixed size cells. For every model iteration, each cell acts only in relation to the influence of its immediate neighbours in accordance with appropriate rules. The model presented here takes approximations of existing flow and sediment transport equations, and integrates them, together with slope and floodplain approximations, within a cellular automaton framework. This method has been applied to the basin of Cam Gill Beck (4.2 km2 above Starbotton, upper Wharfedale, a tributary of the River Wharfe, North Yorkshire, UK. This approach provides, for the first time, a workable model of the whole basin at a 1 m resolution. Preliminary results show the evolution of bars, braids, terraces and alluvial fans which are similar to those observed in the field, and examples of large and small scale non-linear behaviour which may have considerable implications for future models.

  13. Advanced spatial metrics analysis in cellular automata land use and cover change modeling

    International Nuclear Information System (INIS)

    This paper proposes an approach for a more effective definition of cellular automata transition rules for landscape change modeling using an advanced spatial metrics analysis. This approach considers a four-stage methodology based on: (i) the search for the appropriate spatial metrics with minimal correlations; (ii) the selection of the appropriate neighborhood size; (iii) the selection of the appropriate technique for spatial metrics application; and (iv) the analysis of the contribution level of each spatial metric for joint use. The case study uses an initial set of 7 spatial metrics of which 4 are selected for modeling. Results show a better model performance when compared to modeling without any spatial metrics or with the initial set of 7 metrics.

  14. Empirical results for pedestrian dynamics and their implications for cellular automata models

    CERN Document Server

    Schadschneider, Andreas

    2010-01-01

    A large number of models for pedestrian dynamics have been developed over the years. However, so far not much attention has been paid to their quantitative validation. Usually the focus is on the reproduction of empirically observed collective phenomena, as lane formation in counterflow. This can give an indication for the realism of the model, but practical applications, e.g. in safety analysis, require quantitative predictions. We discuss the current experimental situation, especially for the fundamental diagram which is the most important quantity needed for calibration. In addition we consider the implications for the modelling based on cellular automata. As specific example the floor field model is introduced. Apart from the properties of its fundamental diagram we discuss the implications of an egress experiment for the relevance of conflicts and friction effects.

  15. A new three-step cellular automaton model considering a realistic driving decision

    International Nuclear Information System (INIS)

    Most cellular automaton (CA) traffic flow models include four steps and take the velocity as the driver’s main concern. To better understand traffic behaviors, a new three-step CA model is studied, in which a realistic driving decision is divided into three stages: decision-making, action and result. The new model is novel in using the acceleration as a decision variable. It considers the deceleration limitation and proposes the maximum deceleration to be 2 cells per time step, based on real experimental data. Simulation results show that the model can reproduce the synchronized flow effectively and describe the phase transition well. Moreover, it can exhibit metastability and hysteresis if the slow-to-start effect is involved. Finally, a realistic application to systematic flow optimization is analyzed and an interesting result is obtained that a restriction of the inflow can lead to an improvement of the total flow through a bottleneck. (paper)

  16. Modelling of Eutectic Saturation Influence on Microstructure in Thin Wall Ductile Iron Casting Using Cellular Automata

    Directory of Open Access Journals (Sweden)

    M. Górny

    2012-12-01

    Full Text Available The mathematical model of the globular eutectic solidification in 2D was designed. Proposed model is based on the Cellular AutomatonFinite Differences (CA-FD calculation method. Model has been used for studies of the primary austenite and of globular eutectic grainsgrowth during the ductile iron solidification in the thin wall casting. Model takes into account, among other things, non-uniformtemperature distribution in the casting wall cross-section, kinetics of the austenite and graphite grains nucleation, and non-equilibriumnature of the interphase boundary migration. Calculation of eutectic saturation influence (Sc = 0.9 - 1.1 on microstructure (austenite and graphite fraction, density of austenite and graphite grains and temperature curves in 2 mm wall ductile iron casting has been done.

  17. Cellular-automata model of the dwarf shrubs populations and communities dynamics

    Directory of Open Access Journals (Sweden)

    A. S. Komarov

    2015-06-01

    Full Text Available The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area projective cover. The model allows us to investigate the conditions of self-maintenance and sustainability population under different environmental conditions (inaccessibility of the territory for settlement, mosaic moisture conditions of soil and wealth. The model provides a forecast of the total biomass dynamics shrubs and their fractions (stems, leaves, roots, fine roots, fruits on the basis of the data obtained in the discrete description of ontogenesis and further information on the productivity of the plant fractions. The inclusion of the joint dynamics of biomass of shrubs and soil in EFIMOD models cycle of carbon and nitrogen to evaluate the role of shrubs in these circulations, especially at high impact, such as forest fires and clear cutting, allow forecasting of the dynamics of populations and ecosystem functions of shrubs (regulation of biogeochemical cycles maintaining biodiversity, participation in the creation of non-wood products with changing climatic conditions and strong damaging effects (logging, fires; and application of the models developed to investigate the stability and productivity of shrubs and their participation in the cycle of carbon and nitrogen in different climatic and edaphic conditions.

  18. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.; Zilles, Sandra

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were...

  19. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.;

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were...

  20. Modeling of hydrogen interactions with beryllium

    Energy Technology Data Exchange (ETDEWEB)

    Longhurst, G.R. [Lockheed Martin Idaho Technologies Co., Idaho Falls, ID (United States)

    1998-01-01

    In this paper, improved mathematical models are developed for hydrogen interactions with beryllium. This includes the saturation effect observed for high-flux implantation of ions from plasmas and retention of tritium produced from neutronic transmutations in beryllium. Use of the models developed is justified by showing how they can replicated experimental data using the TMAP4 tritium transport code. (author)

  1. Cellular automata model based on GIS and urban sprawl dynamics simulation

    Science.gov (United States)

    Mu, Fengyun; Zhang, Zengxiang

    2005-10-01

    The simulation of land use change process needs the support of Geographical Information System (GIS) and other relative technologies. While the present commercial GIS lack capabilities of distribution, prediction, and simulation of spatial-temporal data. Cellular automata (CA) provide dynamically modeling "from bottom-to-top" framework and posses the capability of modeling spatial-temporal evolvement process of a complicated geographical system, which is composed of a fourfold: cells, states, neighbors and rules. The simplicity and flexibility make CA have the ability to simulate a variety of behaviors of complex systems. One of the most potentially useful applications of cellular automata from the point of view of spatial planning is their use in simulations of urban sprawl at local and regional level. The paper firstly introduces the principles and characters of the cellular automata, and then discusses three methods of the integration of CA and GIS. The paper analyses from a practical point of view the factors that effect urban activities in the science of spatial decision-making. The status of using CA to dynamic simulates of urban expansion at home and abroad is analyzed. Finally, the problems and tendencies that exist in the application of CA model are detailed discussed, such as the quality of the data that the CA needs, the self-organization of the CA roots in the mutual function among the elements of the system, the partition of the space scale, the time calibration of the CA and the integration of the CA with other modular such as artificial nerve net modular and population modular etc.

  2. A cardiac electrical activity model based on a cellular automata system in comparison with neural network model.

    Science.gov (United States)

    Khan, Muhammad Sadiq Ali; Yousuf, Sidrah

    2016-03-01

    Cardiac Electrical Activity is commonly distributed into three dimensions of Cardiac Tissue (Myocardium) and evolves with duration of time. The indicator of heart diseases can occur randomly at any time of a day. Heart rate, conduction and each electrical activity during cardiac cycle should be monitor non-invasively for the assessment of "Action Potential" (regular) and "Arrhythmia" (irregular) rhythms. Many heart diseases can easily be examined through Automata model like Cellular Automata concepts. This paper deals with the different states of cardiac rhythms using cellular automata with the comparison of neural network also provides fast and highly effective stimulation for the contraction of cardiac muscles on the Atria in the result of genesis of electrical spark or wave. The specific formulated model named as "States of automaton Proposed Model for CEA (Cardiac Electrical Activity)" by using Cellular Automata Methodology is commonly shows the three states of cardiac tissues conduction phenomena (i) Resting (Relax and Excitable state), (ii) ARP (Excited but Absolutely refractory Phase i.e. Excited but not able to excite neighboring cells) (iii) RRP (Excited but Relatively Refractory Phase i.e. Excited and able to excite neighboring cells). The result indicates most efficient modeling with few burden of computation and it is Action Potential during the pumping of blood in cardiac cycle. PMID:27087101

  3. Web-based Interactive Landform Simulation Model - Grand Canyon

    Science.gov (United States)

    Luo, W.; Pelletier, J. D.; Duffin, K.; Ormand, C. J.; Hung, W.; Iverson, E. A.; Shernoff, D.; Zhai, X.; Chowdary, A.

    2013-12-01

    Earth science educators need interactive tools to engage and enable students to better understand how Earth systems work over geologic time scales. The evolution of landforms is ripe for interactive, inquiry-based learning exercises because landforms exist all around us. The Web-based Interactive Landform Simulation Model - Grand Canyon (WILSIM-GC, http://serc.carleton.edu/landform/) is a continuation and upgrade of the simple cellular automata (CA) rule-based model (WILSIM-CA, http://www.niu.edu/landform/) that can be accessed from anywhere with an Internet connection. Major improvements in WILSIM-GC include adopting a physically based model and the latest Java technology. The physically based model is incorporated to illustrate the fluvial processes involved in land-sculpting pertaining to the development and evolution of one of the most famous landforms on Earth: the Grand Canyon. It is hoped that this focus on a famous and specific landscape will attract greater student interest and provide opportunities for students to learn not only how different processes interact to form the landform we observe today, but also how models and data are used together to enhance our understanding of the processes involved. The latest development in Java technology (such as Java OpenGL for access to ubiquitous fast graphics hardware, Trusted Applet for file input and output, and multithreaded ability to take advantage of modern multi-core CPUs) are incorporated into building WILSIM-GC and active, standards-aligned curricula materials guided by educational psychology theory on science learning will be developed to accompany the model. This project is funded NSF-TUES program.

  4. Micropatterned co-culture of hepatocyte spheroids layered on non-parenchymal cells to understand heterotypic cellular interactions

    International Nuclear Information System (INIS)

    Microfabrication and micropatterning techniques in tissue engineering offer great potential for creating and controlling cellular microenvironments including cell–matrix interactions, soluble stimuli and cell–cell interactions. Here, we present a novel approach to generate layered patterning of hepatocyte spheroids on micropatterned non-parenchymal feeder cells using microfabricated poly(ethylene glycol) (PEG) hydrogels. Micropatterned PEG-hydrogel-treated substrates with two-dimensional arrays of gelatin circular domains (ϕ = 100 μm) were prepared by photolithographic method. Only on the critical structure of PEG hydrogel with perfect protein rejection, hepatocytes were co-cultured with non-parenchymal cells to be led to enhanced hepatocyte functions. Then, we investigated the mechanism of the functional enhancement in co-culture with respect to the contributions of soluble factors and direct cell–cell interactions. In particular, to elucidate the influence of soluble factors on hepatocyte function, hepatocyte spheroids underlaid with fibroblasts (NIH/3T3 mouse fibroblasts) or endothelial cells (BAECs: bovine aortic endothelial cells) were compared with physically separated co-culture of hepatocyte monospheroids with NIH3T3 or BAEC using trans-well culture systems. Our results suggested that direct heterotypic cell-to-cell contact and soluble factors, both of these between hepatocytes and fibroblasts, significantly enhanced hepatocyte functions. In contrast, direct heterotypic cell-to-cell contact between hepatocytes and endothelial cells only contributed to enhance hepatocyte functions. This patterning technique can be a useful experimental tool for applications in basic science, drug screening and tissue engineering, as well as in the design of artificial liver devices. (paper)

  5. Interacting Dark Energy Models -- Scalar Linear Perturbations

    CERN Document Server

    Perico, E L D

    2016-01-01

    We extend the dark sector interacting models assuming the dark energy as the sum of independent contributions $\\rho_{\\Lambda} =\\sum_i\\rho_{\\Lambda i}$, associated with (and interacting with) each of the $i$ material species. We derive the linear scalar perturbations for two interacting dark energy scenarios, modeling its cosmic evolution and identifying their different imprints in the CMB and matter power spectrum. Our treatment was carried out for two phenomenological motivated expressions of the dark energy density, $\\rho_\\Lambda(H^2)$ and $\\rho_\\Lambda(R)$. The $\\rho_\\Lambda(H^2)$ description turned out to be a full interacting model, i.e., the dark energy interacts with everyone material species in the universe, whereas the $\\rho_\\Lambda(R)$ description only leads to interactions between dark energy and the non-relativistic matter components; which produces different imprints of the two models on the matter power spectrum. A comparison with the Planck 2015 data was made in order to constrain the free para...

  6. Modeling of soil-water-structure interaction

    DEFF Research Database (Denmark)

    Tang, Tian

    variations as well as the developed nonlinear soil displacements and stresses under monotonic and cyclic loading. With the FVM nonlinear coupled soil models as a basis, multiphysics modeling of wave-seabed-structure interaction is carried out. The computations are done in an open source code environment......The trend towards the installation of more offshore constructions for the production and transmission of marine oil, gas and wind power is expected to continue over the coming years. An important process in the offshore construction design is the assessment of seabed soil stability exposed to...... dynamic ocean waves. The goal of this research project is to develop numerical soil models for computing realistic seabed response in the interacting offshore environment, where ocean waves, seabed and offshore structure highly interact with each other. The seabed soil models developed are based on the...

  7. Cellular Automata

    OpenAIRE

    Bagnoli, Franco

    1998-01-01

    An introduction to cellular automata (both deterministic and probabilistic) with examples. Definition of deterministic automata, dynamical properties, damage spreading and Lyapunov exponents; probabilistic automata and Markov processes, nonequilibrium phase transitions, directed percolation, diffusion; simulation techniques, mean field. Investigation themes: life, epidemics, forest fires, percolation, modeling of ecosystems and speciation. They represent my notes for the school "Dynamical Mod...

  8. Case Study of Phase Transition in Cellular Models of Pedestrian Flow

    Czech Academy of Sciences Publication Activity Database

    Bukáček, M.; Hrabák, Pavel

    Cham : Springer, 2014 - (Was, J.; Sirakoulis, G.; Bandini, S.), s. 508-517 ISBN 978-3-319-11519-1. ISSN 0302-9743. - (Lecture Notes in Computer Science. 8751). [ACRI 2014. International Conference on Cellular Automata for Research and Industry /11./. Krakov (PL), 22.09.2014-25.09.2014] R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Floor field model * phase transition * travel time * bounds principle * asynchronous update Subject RIV: IN - Informatics, Computer Science http://library.utia.cas.cz/separaty/2014/AS/hrabak-0432244.pdf

  9. Metabolically active portion of fat-free mass: a cellular body composition level modeling analysis

    OpenAIRE

    Wang, ZiMian; Heshka, Stanley; Wang, Jack; Gallagher, Dympna; Deurenberg, Paul; Chen, Zhao; Heymsfield, Steven B

    2006-01-01

    The proportion of fat-free mass (FFM) as body cell mass (BCM) is highly related to whole body resting energy expenditure. However, the magnitude of BCM/FFM may have been underestimated in previous studies. This is because Moore’s equation [BCM (kg) =0.00833 × total body potassium (in mmol)], which was used to predict BCM, underestimates BCM by ~ %. The aims of the present study were to develop a theoretical BCM/FFM model at the cellular level and to explore the influences of sex, age, and adi...

  10. Driver’s Awareness and Lane Changing Maneuver in Traffic Flow based on Cellular Automaton Model

    OpenAIRE

    Kohei Arai; Steven Ray Sentinuwo

    2015-01-01

    Effect of driver’s awareness (e.g., to estimate the speed and arrival time of another vehicle) on the lane changing maneuver is discussed. “Scope awareness” is defined as the visibility which is required for the driver to make a visual perception about road condition and the speed of vehicle that appears in the target lane for lane changing in the road. Cellular automaton based simulation model is created and applied to simulation studies for driver awareness behavior. This study clarifies re...

  11. A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

    Science.gov (United States)

    Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi

    2015-08-01

    Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.

  12. Transition between immune and disease states in a cellular automaton model of clonal immune response

    CERN Document Server

    Bezzi, M; Ruffo, S; Seiden, P E; Bezzi, Michele; Celada, Franco; Ruffo, Stefano; Seiden, Philip E.

    1997-01-01

    In this paper we extend the Celada-Seiden (CS) model of the humoral immune response to include infectious virus and cytotoxic T lymphocytes (cellular response). The response of the system to virus involves a competition between the ability of the virus to kill the host cells and the host's ability to eliminate the virus. We find two basins of attraction in the dynamics of this system, one is identified with disease and the other with the immune state. There is also an oscillating state that exists on the border of these two stable states. Fluctuations in the population of virus or antibody can end the oscillation and drive the system into one of the stable states. The introduction of mechanisms of cross-regulation between the two responses can bias the system towards one of them. We also study a mean field model, based on coupled maps, to investigate virus-like infections. This simple model reproduces the attractors for average populations observed in the cellular automaton. All the dynamical behavior connect...

  13. An implementation of cellular automaton model for single-line train working diagram

    Institute of Scientific and Technical Information of China (English)

    Hua Wei; Liu Jun

    2006-01-01

    According to the railway transportation system's characteristics,a new cellular automaton model for the singleline railway system is presented in this paper.Based on this model,several simulations were done to imitate the train operation under three working diagrams.From a different angle the results show how the organization of train operation impacts on the railway carrying capacity.By using the non-parallel train working diagram the influence of fast-train on slow-train is found to be the strongest.Many slow-trains have to wait in-between neighbouring stations to let the fast-train(s) pass through first.So the slow-train will advance like a wave propagating from the departure station to the arrival station.This also resembles the situation of a highway jammed traffic flow.Furthermore,the nonuniformity of travel times between the sections also greatly limits the railway carrying capacity.After converting the nonuniform sections into the sections with uniform travel times while the total travel time is kept unchanged,all three carrying capacities are improved greatly as shown by simulation.It also shows that the cellular automaton model is an effective and feasible way to investigate the railway transDortation system.

  14. Cranking model and attenuation of Coriolis interaction

    International Nuclear Information System (INIS)

    Description of rotational bands of odd deformed nuclei in the self-consistent Cranking model (SCM) is given. Causes of attenuation of the Coriolis interaction in the nuclei investigated are studied, and account of bound of one-particle degrees of freedom with rotation of the Hartree-Fock-Bogolyubov (HFB) self-consistent method is introduced additionally to SCM for qualitative agreement with experimental data. Merits and shortages of SCM in comparison with the quadruparticle-rotor (QR) model are discussed. All know ways for constructing the Hamiltonian QR model (or analog of such Hamiltonian) on the basis of the microscopic theory are shown to include two more approximations besides others: quasi-particle-rotational interaction leading to pair break is taken into account in the second order of the perturbation theory; some exchange diagrams are neglected among diagrams of the second order according to this interaction. If one makes the same approximations in SCM instead of HFB method, then the dependence of level energies on spin obtained in this case is turned out to be close to the results of the QR model. Besides, the problem on renormalization of matrix elements of quasi-rotational interaction occurs in such nonself-consistent approach as in the QR model. In so far as the similar problem does not occur in SCM, one can make the conclusion that the problem of attenuation of Coriolis interaction involves the approximations given above

  15. Bigraphical models for protein and membrane interactions

    CERN Document Server

    Bacci, Giorgio; Miculan, Marino; 10.4204/EPTCS.11.1

    2009-01-01

    We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes.

  16. Independent pair parton interactions model of hadron interactions

    Science.gov (United States)

    Dremin, I. M.; Nechitailo, V. A.

    2004-08-01

    A model of independent pair parton interactions is proposed, according to which hadron interactions are represented by a set of independent binary parton collisions. The final multiplicity distribution is described by a convolution of the negative binomial distributions in each of the partonic collisions. As a result, it is given by a weighted sum of negative binomial distributions with parameters multiplied by the number of active pairs. Its shape and moments are considered. Experimental data on multiplicity distributions in high energy pp¯ processes are well fitted by these distributions. Predictions for the CERN Large Hadron Collider and higher energies are presented. The difference between e+e- and pp¯ processes is discussed.

  17. An analysis of penalized interaction models

    OpenAIRE

    Zhao, Junlong; Leng, Chenlei

    2016-01-01

    An important consideration for variable selection in interaction models is to design an appropriate penalty that respects hierarchy of the importance of the variables. A common theme is to include an interaction term only after the corresponding main effects are present. In this paper, we study several recently proposed approaches and present a unified analysis on the convergence rate for a class of estimators, when the design satisfies the restricted eigenvalue condition. In particular, we s...

  18. Microscopic Models of Heavy Ion Interactions

    OpenAIRE

    Capella, A.

    2003-01-01

    An introduction to dynamical microscopic models of hadronic and nuclear interactions is presented. Special emphasis is put in the relation between multiparticle production and total cross-section contributions. In heavy ion collisions, some observables, considered as signals of the production of a Quark Gluon Plasma (QGP), are studied. It is shown that they can only be described if final state interactions are introduced. It is argued that the cross-sections required are too small to drive th...

  19. Model of Interaction between Learning and Evolution

    OpenAIRE

    Red'ko, Vladimir G.

    2014-01-01

    The model of interaction between learning and evolutionary optimization is designed and investigated. The evolving population of modeled organisms is considered. The mechanism of the genetic assimilation of the acquired features during a number of generations of Darwinian evolution is studied. It is shown that the genetic assimilation takes place as follows: phenotypes of modeled organisms move towards the optimum at learning; then the selection takes place; genotypes of selected organisms al...

  20. Modeling of the competition life cycle using the software complex of cellular automata PyCAlab

    Science.gov (United States)

    Berg, D. B.; Beklemishev, K. A.; Medvedev, A. N.; Medvedeva, M. A.

    2015-11-01

    The aim of the work is to develop a numerical model of the life cycle of competition on the basis of software complex cellular automata PyCAlab. The model is based on the general patterns of growth of various systems in resource-limited settings. At examples it is shown that the period of transition from an unlimited growth of the market agents to the stage of competitive growth takes quite a long time and may be characterized as monotonic. During this period two main strategies of competitive selection coexist: 1) capture of maximum market space with any reasonable costs; 2) saving by reducing costs. The obtained results allow concluding that the competitive strategies of companies must combine two mentioned types of behavior, and this issue needs to be given adequate attention in the academic literature on management. The created numerical model may be used for market research when developing of the strategies for promotion of new goods and services.

  1. A Two-Lane Cellular Automata Model with Influence of Next-Nearest Neighbor Vehicle

    International Nuclear Information System (INIS)

    In this paper, we propose a new two-lane cellular automata model in which the influence of the next-nearest neighbor vehicle is considered. The attributes of the traffic system composed of fast-lane and slow-lane are investigated by the new traffic model. The simulation results show that the proposed two-lane traffic model can reproduce some traffic phenomena observed in real traffic, and that maximum flux and critical density are close to the field measurements. Moreover, the initial density distribution of the fast-lane and slow-lane has much influence on the traffic flow states. With the ratio between the densities of slow lane and fast lane increasing the lane changing frequency increases, but maximum flux decreases. Finally, the influence of the sensitivity coefficients is discussed.

  2. Designing a mathematical model for integrating dynamic cellular manufacturing into supply chain system

    Science.gov (United States)

    Aalaei, Amin; Davoudpour, Hamid

    2012-11-01

    This article presents designing a new mathematical model for integrating dynamic cellular manufacturing into supply chain system with an extensive coverage of important manufacturing features consideration of multiple plants location, multi-markets allocation, multi-period planning horizons with demand and part mix variation, machine capacity, and the main constraints are demand of markets satisfaction in each period, machine availability, machine time-capacity, worker assignment, available time of worker, production volume for each plant and the amounts allocated to each market. The aim of the proposed model is to minimize holding and outsourcing costs, inter-cell material handling cost, external transportation cost, procurement & maintenance and overhead cost of machines, setup cost, reconfiguration cost of machines installation and removal, hiring, firing and salary worker costs. Aimed to prove the potential benefits of such a design, presented an example is shown using a proposed model.

  3. A mathematical model in cellular manufacturing system considering subcontracting approach under constraints

    Directory of Open Access Journals (Sweden)

    Kamran Forghani

    2012-10-01

    Full Text Available In this paper, a new mathematical model in cellular manufacturing systems (CMSs has been presented. In order to increase the performance of manufacturing system, the production quantity of parts has been considered as a decision variable, i.e. each part can be produced and outsourced, simultaneously. This extension would be minimized the unused capacity of machines. The exceptional elements (EEs are taken into account and would be totally outsourced to the external supplier in order to remove intercellular material handling cost. The problem has been formulated as a mixed-integer programming to minimize the sum of manufacturing variable costs under budget, machines capacity and demand constraints. Also, to evaluate advantages of the model, several illustrative numerical examples have been provided to compare the performance of the proposed model with the available classical approaches in the literature.

  4. Steady state speed distribution analysis for a combined cellular automaton traffic model

    Institute of Scientific and Technical Information of China (English)

    Wang Jun-Feng; Chen Gui-Sheng; Liu Jin

    2008-01-01

    Cellular Automaton (CA) baaed traffic flow models have been extensively studied due to their effectiveness and simplicity in recent years. This paper develops a discrete time Markov chain (DTMC) analytical framework for a Nagel-Schreckenberg and Fukui-Ishibashi combined CA model (W2H traffic flow model) from microscopic point of view to capture the macroscopic steady state speed distributions. The inter-vehicle spacing Markov chain and the steady state speed Markov chain are proved to be irreducible and ergodie. The theoretical speed probability distributions depending on the traffic density and stochastic delay probability are in good accordance with numerical simulations. The derived fundamental diagram of the average speed from theoretical speed distributions is equivalent to the results in the previous work.

  5. Combined modeling of cell aggregation and adhesion mediated by receptor–ligand interactions under shear flow

    Directory of Open Access Journals (Sweden)

    Yu Du

    2015-11-01

    Full Text Available Blood cell aggregation and adhesion to endothelial cells under shear flow are crucial to many biological processes such as thrombi formation, inflammatory cascade, and tumor metastasis, in which these cellular interactions are mainly mediated by the underlying receptor–ligand bindings. While theoretical modeling of aggregation dynamics and adhesion kinetics of interacting cells have been well studied separately, how to couple these two processes remains unclear. Here we develop a combined model that couples cellular aggregation dynamics and adhesion kinetics under shear flow. The impacts of shear rate (or shear stress and molecular binding affinity were elucidated. This study provides a unified model where the action of a fluid flow drives cell aggregation and adhesion under the modulations of the mechanical shear flow and receptor–ligand interaction kinetics. It offers an insight into understanding the relevant biological processes and functions.

  6. Using a Cellular Automata-Markov Model to Reconstruct Spatial Land-Use Patterns in Zhenlai County, Northeast China

    Directory of Open Access Journals (Sweden)

    Yuanyuan Yang

    2015-05-01

    Full Text Available Decadal to centennial land use and land cover change has been consistently singled out as a key element and an important driver of global environmental change, playing an essential role in balancing energy use. Understanding long-term human-environment interactions requires historical reconstruction of past land use and land cover changes. Most of the existing historical reconstructions have insufficient spatial and thematic detail and do not consider various land change types. In this context, this paper explored the possibility of using a cellular automata-Markov model in 90 m × 90 m spatial resolution to reconstruct historical land use in the 1930s in Zhenlai County, China. Then the three-map comparison methodology was employed to assess the predictive accuracy of the transition modeling. The model could produce backward projections by analyzing land use changes in recent decades, assuming that the present land use pattern is dynamically dependent on the historical one. The reconstruction results indicated that in the 1930s most of the study area was occupied by grasslands, followed by wetlands and arable land, while other land categories occupied relatively small areas. Analysis of the three-map comparison illustrated that the major differences among the three maps have less to do with the simulation model and more to do with the inconsistencies among the land categories during the study period. Different information provided by topographic maps and remote sensing images must be recognized.

  7. Quark Interchange Model of Baryon Interactions.

    Science.gov (United States)

    Maslow, Joel Neal

    The strong interactions at low energy are traditionally described by meson field theories treating hadrons as point -like particles. Here a mesonic quark interchange model (QIM) is presented which takes into account the finite size of the baryons and the internal quark structure of hadrons. The model incorporates the basic quark-gluon coupling of quantum chromodynamics (QCD) and the MIT bag model for color confinement. Because the quark-gluon coupling constant is large and we assume that confinement excludes overlap of hadronic quark bags except at high momenta, a non-perturbative method of nuclear interactions is presented. The QIM allows for exchange of quark quantum numbers at the bag boundary between colliding hadrons mediated at short distances by a gluon exchange between two quarks within the hadronic interior. This generates, via a Fierz transformation, an effective space-like t channel exchange of color singlet (qq) states that can be identified with the low lying meson multiplets. Thus, a one boson exchange (OBE) model is obtained that allows for comparison with traditional phenomenological models of nuclear scattering. Inclusion of strange quarks enables calculation of Yn scattering. The NN and YN coupling constants and the nucleon form factors show good agreement with experimental values as do the deuteron low energy data and the NN low energy phase shifts. Thus, the QIM provides a simple model of strong interactions that is chirally invariant, includes confinement and allows for an OBE form of hadronic interaction at low energies and momentum transfers.

  8. Quark interchange model of baryon interactions

    International Nuclear Information System (INIS)

    The strong interactions at low energy are traditionally described by meson field theories treating hadrons as point-like particles. Here a mesonic quark interchange model (QIM) is presented which takes into account the finite size of the baryons and the internal quark structure of hadrons. The model incorporates the basic quark-gluon coupling of quantum chromodynamics (QCD) and the MIT bag model for color confinement. Because the quark-gluon coupling constant is large and it is assumed that confinement excludes overlap of hadronic quark bags except at high momenta, a non-perturbative method of nuclear interactions is presented. The QIM allows for exchange of quark quantum numbers at the bag boundary between colliding hadrons mediated at short distances by a gluon exchange between two quarks within the hadronic interior. This generates, via a Fierz transformation, an effective space-like t channel exchange of color singlet (q anti-q) states that can be identified with the low lying meson multiplets. Thus, a one boson exchange (OBE) model is obtained that allows for comparison with traditional phenomenological models of nuclear scattering. Inclusion of strange quarks enables calculation of YN scattering. The NN and YN coupling constants and the nucleon form factors show good agreement with experimental values as do the deuteron low energy data and the NN low energy phase shifts. Thus, the QIM provides a simple model of strong interactions that is chirally invariant, includes confinement and allows for an OBE form of hadronic interaction at low energies and momentum transfers

  9. Quark interchange model of baryon interactions

    Energy Technology Data Exchange (ETDEWEB)

    Maslow, J.N.

    1983-01-01

    The strong interactions at low energy are traditionally described by meson field theories treating hadrons as point-like particles. Here a mesonic quark interchange model (QIM) is presented which takes into account the finite size of the baryons and the internal quark structure of hadrons. The model incorporates the basic quark-gluon coupling of quantum chromodynamics (QCD) and the MIT bag model for color confinement. Because the quark-gluon coupling constant is large and it is assumed that confinement excludes overlap of hadronic quark bags except at high momenta, a non-perturbative method of nuclear interactions is presented. The QIM allows for exchange of quark quantum numbers at the bag boundary between colliding hadrons mediated at short distances by a gluon exchange between two quarks within the hadronic interior. This generates, via a Fierz transformation, an effective space-like t channel exchange of color singlet (q anti-q) states that can be identified with the low lying meson multiplets. Thus, a one boson exchange (OBE) model is obtained that allows for comparison with traditional phenomenological models of nuclear scattering. Inclusion of strange quarks enables calculation of YN scattering. The NN and YN coupling constants and the nucleon form factors show good agreement with experimental values as do the deuteron low energy data and the NN low energy phase shifts. Thus, the QIM provides a simple model of strong interactions that is chirally invariant, includes confinement and allows for an OBE form of hadronic interaction at low energies and momentum transfers.

  10. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

    Directory of Open Access Journals (Sweden)

    Drubin David

    2011-10-01

    Full Text Available Abstract Background Humans and other organisms are equipped with a set of responses that can prevent damage from exposure to a multitude of endogenous and environmental stressors. If these stress responses are overwhelmed, this can result in pathogenesis of diseases, which is reflected by an increased development of, e.g., pulmonary and cardiac diseases in humans exposed to chronic levels of environmental stress, including inhaled cigarette smoke (CS. Systems biology data sets (e.g., transcriptomics, phosphoproteomics, metabolomics could enable comprehensive investigation of the biological impact of these stressors. However, detailed mechanistic networks are needed to determine which specific pathways are activated in response to different stressors and to drive the qualitative and eventually quantitative assessment of these data. A current limiting step in this process is the availability of detailed mechanistic networks that can be used as an analytical substrate. Results We have built a detailed network model that captures the biology underlying the physiological cellular response to endogenous and exogenous stressors in non-diseased mammalian pulmonary and cardiovascular cells. The contents of the network model reflect several diverse areas of signaling, including oxidative stress, hypoxia, shear stress, endoplasmic reticulum stress, and xenobiotic stress, that are elicited in response to common pulmonary and cardiovascular stressors. We then tested the ability of the network model to identify the mechanisms that are activated in response to CS, a broad inducer of cellular stress. Using transcriptomic data from the lungs of mice exposed to CS, the network model identified a robust increase in the oxidative stress response, largely mediated by the anti-oxidant NRF2 pathways, consistent with previous reports on the impact of CS exposure in the mammalian lung. Conclusions The results presented here describe the construction of a cellular stress

  11. Use of Computational Modeling to Evaluate Hypotheses About the Molecular and Cellular Mechanisms of Bystander Effects

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Yuchao; Conolly, Rory B; Andersen, Melvin E.

    2006-11-21

    This report describes the development of a computational systems biology approach to evaluate the hypotheses of molecular and cellular mechanisms of adaptive response to low dose ionizing radiation. Our concept is that computational models of signaling pathways can be developed and linked to biologically based dose response models to evaluate the underlying molecular mechanisms which lead to adaptive response. For development of quantitatively accurate, predictive models, it will be necessary to describe tissues consisting of multiple cell types where the different types each contribute in their own way to the overall function of the tissue. Such a model will probably need to incorporate not only cell type-specific data but also spatial information on the architecture of the tissue and on intercellular signaling. The scope of the current model was more limited. Data obtained in a number of different biological systems were synthesized to describe a chimeric, “average” population cell. Biochemical signaling pathways involved in sensing of DNA damage and in the activation of cell cycle checkpoint controls and the apoptotic path were also included. As with any computational modeling effort, it was necessary to develop these simplified initial descriptions (models) that can be iteratively refined. This preliminary model is a starting point which, with time, can evolve to a level of refinement where large amounts of detailed biological information are synthesized and a capability for robust predictions of dose- and time-response behaviors is obtained.

  12. A Vector-based Cellular Automata Model for Simulating Urban Land Use Change

    Institute of Scientific and Technical Information of China (English)

    LU Yi; CAO Min; ZHANG Lei

    2015-01-01

    Cellular Automata (CA) is widely used for the simulation of land use changes.This study applied a vector-based CA model to simulate land use change in order to minimize or eliminate the scale sensitivity in traditional raster-based CA model.The cells of vector-based CA model are presented according to the shapes and attributes of geographic entities,and the transition rules of vector-based CA model are improved by taking spatial variables of the study area into consideration.The vector-based CA model is applied to simulate land use changes in downtown of Qidong City,Jiangsu Province,China and its validation is confirmed by the methods of visual assessment and spatial accuracy.The simulation result of vector-based CA model reveals that nearly 75% of newly increased urban cells are located in the northwest and southwest parts of the study area from 2002 to 2007,which is in consistent with real land use map.In addition,the simulation results of the vector-based and raster-based CA models are compared to real land use data and their spatial accuracies are found to be 84.0% and 81.9%,respectively.In conclusion,results from this study indicate that the vector-based CA model is a practical and applicable method for the simulation of urbanization processes.

  13. SOFTWARE RELIABILITY MODEL FOR COMPONENT INTERACTION MODE

    Institute of Scientific and Technical Information of China (English)

    Wang Qiang; Lu Yang; Xu Zijun; Han Jianghong

    2011-01-01

    With the rapid progress of component technology,the software development methodology of gathering a large number of components for designing complex software systems has matured.But,how to assess the application reliability accurately with the information of system architecture and the components reliabilities together has become a knotty problem.In this paper,the defects in formal description of software architecture and the limitations in existed model assumptions are both analyzed.Moreover,a new software reliability model called Component Interaction Mode (CIM) is proposed.With this model,the problem for existed component-based software reliability analysis models that cannot deal with the cases of component interaction with non-failure independent and non-random control transition is resolved.At last,the practice examples are presented to illustrate the effectiveness of this model

  14. Geographic Spatiotemporal Dynamic Model using Cellular Automata and Data Mining Techniques

    Directory of Open Access Journals (Sweden)

    Ahmad Zuhdi

    2011-05-01

    Full Text Available Geospatial data and information availability has been increasing rapidly and has provided users with knowledge on entities change and movement in a system. Cellular Geography model applies Cellular Automata on Geographic data by defining transition rules to the data grid. This paper presents the techniques for extracting transition rule(s from time series data grids, using multiple linear regression analysis. Clustering technique is applied to minimize the number of transition rules, which can be offered and chosen to change a new unknown grid. Each centroid of a cluster is associated with a transition rule and a grid of data. The chosen transition rule is associated with grid that has a minimum distance to the new data grid to be simulated. Validation of the model can be provided either quantitatively through an error measurement or qualitatively by visualizing the result of the simulation process. The visualization can also be more informative by adding the error information. Increasing number of cluster may give possibility to improve the simulation accuracy.

  15. Oleuropein Prevents Neuronal Death, Mitigates Mitochondrial Superoxide Production and Modulates Autophagy in a Dopaminergic Cellular Model.

    Science.gov (United States)

    Achour, Imène; Arel-Dubeau, Anne-Marie; Renaud, Justine; Legrand, Manon; Attard, Everaldo; Germain, Marc; Martinoli, Maria-Grazia

    2016-01-01

    Parkinson's disease (PD) is a progressive neurodegenerative disorder, primarily affecting dopaminergic neurons in the substantia nigra. There is currently no cure for PD and present medications aim to alleviate clinical symptoms, thus prevention remains the ideal strategy to reduce the prevalence of this disease. The goal of this study was to investigate whether oleuropein (OLE), the major phenolic compound in olive derivatives, may prevent neuronal degeneration in a cellular dopaminergic model of PD, differentiated PC12 cells exposed to the potent parkinsonian toxin 6-hydroxydopamine (6-OHDA). We also investigated OLE's ability to mitigate mitochondrial oxidative stress and modulate the autophagic flux. Our results obtained by measuring cytotoxicity and apoptotic events demonstrate that OLE significantly decreases neuronal death. OLE could also reduce mitochondrial production of reactive oxygen species resulting from blocking superoxide dismutase activity. Moreover, quantification of autophagic and acidic vesicles in the cytoplasm alongside expression of specific autophagic markers uncovered a regulatory role for OLE against autophagic flux impairment induced by bafilomycin A1. Altogether, our results define OLE as a neuroprotective, anti-oxidative and autophagy-regulating molecule, in a neuronal dopaminergic cellular model. PMID:27517912

  16. Oleuropein Prevents Neuronal Death, Mitigates Mitochondrial Superoxide Production and Modulates Autophagy in a Dopaminergic Cellular Model

    Directory of Open Access Journals (Sweden)

    Imène Achour

    2016-08-01

    Full Text Available Parkinson’s disease (PD is a progressive neurodegenerative disorder, primarily affecting dopaminergic neurons in the substantia nigra. There is currently no cure for PD and present medications aim to alleviate clinical symptoms, thus prevention remains the ideal strategy to reduce the prevalence of this disease. The goal of this study was to investigate whether oleuropein (OLE, the major phenolic compound in olive derivatives, may prevent neuronal degeneration in a cellular dopaminergic model of PD, differentiated PC12 cells exposed to the potent parkinsonian toxin 6-hydroxydopamine (6-OHDA. We also investigated OLE’s ability to mitigate mitochondrial oxidative stress and modulate the autophagic flux. Our results obtained by measuring cytotoxicity and apoptotic events demonstrate that OLE significantly decreases neuronal death. OLE could also reduce mitochondrial production of reactive oxygen species resulting from blocking superoxide dismutase activity. Moreover, quantification of autophagic and acidic vesicles in the cytoplasm alongside expression of specific autophagic markers uncovered a regulatory role for OLE against autophagic flux impairment induced by bafilomycin A1. Altogether, our results define OLE as a neuroprotective, anti-oxidative and autophagy-regulating molecule, in a neuronal dopaminergic cellular model.

  17. A Heuristic Molecular Model of Hydrophobic Interactions

    CERN Document Server

    Hummer, G; García, A E; Pohorille, A; Pratt, L R

    1995-01-01

    Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics of hydrophobic effects and permits important applications to conformational equilibria of nonpolar solutes and hydrophobic residues in biopolymers.

  18. Dynamic computational model suggests that cellular citizenship is fundamental for selective tumor apoptosis.

    Directory of Open Access Journals (Sweden)

    Megan Olsen

    Full Text Available Computational models in the field of cancer research have focused primarily on estimates of biological events based on laboratory generated data. We introduce a novel in-silico technology that takes us to the next level of prediction models and facilitates innovative solutions through the mathematical system. The model's building blocks are cells defined phenotypically as normal or tumor, with biological processes translated into equations describing the life protocols of the cells in a quantitative and stochastic manner. The essentials of communication in a society composed of normal and tumor cells are explored to reveal "protocols" for selective tumor eradication. Results consistently identify "citizenship properties" among cells that are essential for the induction of healing processes in a healthy system invaded by cancer. These properties act via inter-cellular communication protocols that can be optimized to induce tumor eradication along with system recovery. Within the computational systems, the protocols universally succeed in removing a wide variety of tumors defined by proliferation rates, initial volumes, and apoptosis resistant phenotypes; they show high adaptability for biological details and allow incorporation of population heterogeneity. These protocols work as long as at least 32% of cells obey extra-cellular commands and at least 28% of cancer cells report their deaths. This low percentage implies that the protocols are resilient to the suboptimal situations often seen in biological systems. We conclude that our in-silico model is a powerful tool to investigate, to propose, and to exercise logical anti-cancer solutions. Functional results should be confirmed in a biological system and molecular findings should be loaded into the computational model for the next level of directed experiments.

  19. Interaction of cadmium and zinc on accumulation and sub-cellular distribution in leaves of hyperaccumulator Potentilla griffithii

    Energy Technology Data Exchange (ETDEWEB)

    Qiu Rongliang, E-mail: eesqrl@mail.sysu.edu.cn [School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China); Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangzhou 510275 (China); Thangavel, Palaniswamy; Hu Pengjie; Senthilkumar, Palaninaicker; Ying Rongrong [School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China); Tang Yetao [School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China); Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, Guangzhou 510275 (China)

    2011-02-28

    Potentilla griffithii Hook is a newly found hyperaccumulator plant capable of high tolerance and accumulation of Zn and Cd. We investigated the interactive effects between Cd and Zn on accumulation and vacuolar sequestration in P. griffithii. Stimulatory effect of growth was noted at 0.2 mM Cd and 1.25 and 2.5 mM Zn tested. Accumulation of Zn and Cd in roots, petioles and leaves were increased significantly with addition of these metals individually. However, the Zn supplement decreased root Cd accumulation but increased the concentration of Cd in petioles and leaves. The results from sub-cellular distribution showed that up to 94% and 70% of the total Zn and Cd in the leaves were present in the protoplasts, and more than 90% Cd and Zn in the protoplasts were localized in the vacuoles. Nearly, 88% and 85% of total Cd and Zn were extracted in the cell sap of the leaves suggesting that most of the Cd and Zn in the leaves were available in soluble form. The present results indicate that Zn supplement significantly enhanced the petiole accumulation of Cd and further vacuolar sequestration plays an important role in tolerance, detoxification and hyperaccumulation of these metals in P. griffithii.

  20. Interaction of cadmium and zinc on accumulation and sub-cellular distribution in leaves of hyperaccumulator Potentilla griffithii.

    Science.gov (United States)

    Qiu, Rong-Liang; Thangavel, Palaniswamy; Hu, Peng-Jie; Senthilkumar, Palaninaicker; Ying, Rong-Rong; Tang, Ye-Tao

    2011-02-28

    Potentilla griffithii Hook is a newly found hyperaccumulator plant capable of high tolerance and accumulation of Zn and Cd. We investigated the interactive effects between Cd and Zn on accumulation and vacuolar sequestration in P. griffithii. Stimulatory effect of growth was noted at 0.2 mM Cd and 1.25 and 2.5 mM Zn tested. Accumulation of Zn and Cd in roots, petioles and leaves were increased significantly with addition of these metals individually. However, the Zn supplement decreased root Cd accumulation but increased the concentration of Cd in petioles and leaves. The results from sub-cellular distribution showed that up to 94% and 70% of the total Zn and Cd in the leaves were present in the protoplasts, and more than 90% Cd and Zn in the protoplasts were localized in the vacuoles. Nearly, 88% and 85% of total Cd and Zn were extracted in the cell sap of the leaves suggesting that most of the Cd and Zn in the leaves were available in soluble form. The present results indicate that Zn supplement significantly enhanced the petiole accumulation of Cd and further vacuolar sequestration plays an important role in tolerance, detoxification and hyperaccumulation of these metals in P. griffithii. PMID:21211902

  1. A Hsp40 chaperone protein interacts with and modulates the cellular distribution of the primase protein of human cytomegalovirus.

    Directory of Open Access Journals (Sweden)

    Yonggang Pei

    Full Text Available Genomic DNA replication is a universal and essential process for all herpesvirus including human cytomegalovirus (HCMV. HCMV UL70 protein, which is believed to encode the primase activity of the viral DNA replication machinery and is highly conserved among herpesviruses, needs to be localized in the nucleus, the site of viral DNA synthesis. No host factors that facilitate the nuclear import of UL70 have been reported. In this study, we provided the first direct evidence that UL70 specifically interacts with a highly conserved and ubiquitously expressed member of the heat shock protein Hsp40/DNAJ family, DNAJB6, which is expressed as two isoforms, a and b, as a result of alternative splicing. The interaction of UL70 with a common region of DNAJB6a and b was identified by both a two hybrid screen in yeast and coimmunoprecipitation in human cells. In transfected cells, UL70 was primarily co-localized with DNAJB6a in the nuclei and with DNAJB6b in the cytoplasm, respectively. The nuclear import of UL70 was increased in cells in which DNAJB6a was up-regulated or DNAJB6b was down-regulated, and was reduced in cells in which DNAJB6a was down-regulated or DNAJB6b was up-regulated. Furthermore, the level of viral DNA synthesis and progeny production was increased in cells in which DNAJB6a was up-regulated or DNAJB6b was down-regulated, and was reduced in cells in which DNAJB6a was down-regulated or DNAJB6b was up-regulated. Thus, DNAJB6a and b appear to enhance the nuclear import and cytoplasmic accumulation of UL70, respectively. Our results also suggest that the relative expression levels of DNAJB6 isoforms may play a key role in regulating the cellular localization of UL70, leading to modulation of HCMV DNA synthesis and lytic infection.

  2. Cellular Interactions and Biological Responses to Titanium Dioxide Nanoparticles in HepG2 and BEAS-2B Cells: Role of Cell Culture Media

    Science.gov (United States)

    ABSTRACT We have shown previously that the composition of the biological medium used in vitro can affect the cellular interaction and biological response of titanium dioxide nanoparticles (nano-TiO2) in human lung epithelial cells. However, it is unclear if these effects are co...

  3. A Modified Cellular Automaton Approach for Mixed Bicycle Traffic Flow Modeling

    Directory of Open Access Journals (Sweden)

    Xiaonian Shan

    2015-01-01

    Full Text Available Several previous studies have used the Cellular Automaton (CA for the modeling of bicycle traffic flow. However, previous CA models have several limitations, resulting in differences between the simulated and the observed traffic flow features. The primary objective of this study is to propose a modified CA model for simulating the characteristics of mixed bicycle traffic flow. Field data were collected on physically separated bicycle path in Shanghai, China, and were used to calibrate the CA model using the genetic algorithm. Traffic flow features between simulations of several CA models and field observations were compared. The results showed that our modified CA model produced more accurate simulation for the fundamental diagram and the passing events in mixed bicycle traffic flow. Based on our model, the bicycle traffic flow features, including the fundamental diagram, the number of passing events, and the number of lane changes, were analyzed. We also analyzed the traffic flow features with different traffic densities, traffic components on different travel lanes. Results of the study can provide important information for understanding and simulating the operations of mixed bicycle traffic flow.

  4. Idealized Mesoscale Model Simulations of Open Cellular Convection Over the Sea

    DEFF Research Database (Denmark)

    Vincent, Claire Louise; Hahmann, Andrea N.; Kelly, Mark C.

    2012-01-01

    important terms in the budgets were buoyancy, pressure balance and inter-scale transfer to subgrid scales. Cells were also composited to calculate the average cell-scale flow and each of the budget terms on two-dimensional cross-sections through the cells, parallel and perpendicular to the mean wind......The atmospheric conditions during an observed case of open cellular convection over the North Sea were simulated using the Weather Research and Forecasting (WRF) numerical model. Wind, temperature and water vapour mixing ratio profiles from the WRF simulation were used to initialize an idealized...... version of the model, which excluded the effects of topography, surface inhomogeneities and large-scale weather forcing. Cells with an average diameter of 17.4 km developed. Simulations both with and without a capping inversion were made, and the cell-scale kinetic energy budget was calculated for each...

  5. Modeling and Simulation for Urban Rail Traffic Problem Based on Cellular Automata

    Institute of Scientific and Technical Information of China (English)

    许琰; 曹成铉; 李明华; 罗金龙

    2012-01-01

    Based on the Nagel-Schreckenberg model, we propose a new cellular automata model to simulate the urban rail traffic flow under moving block system and present a new minimum instantaneous distance formula under pure moving block. We also analyze the characteristics of the urban rail traffic flow under the influence of train density, station dwell times, the length of train, and the train velocity. Train delays can be decreased effectively through flexible departure intervals according to the preceding train type before its departure. The results demonstrate that a suitable adjustment of the current train velocity based on the following train velocity can greatly shorten the minimum departure intervals and then increase the capacity of rail transit.

  6. Decellularized extracellular matrix microparticles as a vehicle for cellular delivery in a model of anastomosis healing.

    Science.gov (United States)

    Hoganson, David M; Owens, Gwen E; Meppelink, Amanda M; Bassett, Erik K; Bowley, Chris M; Hinkel, Cameron J; Finkelstein, Eric B; Goldman, Scott M; Vacanti, Joseph P

    2016-07-01

    Extracellular matrix (ECM) materials from animal and human sources have become important materials for soft tissue repair. Microparticles of ECM materials have increased surface area and exposed binding sites compared to sheet materials. Decellularized porcine peritoneum was mechanically dissociated into 200 µm microparticles, seeded with fibroblasts and cultured in a low gravity rotating bioreactor. The cells avidly attached and maintained excellent viability on the microparticles. When the seeded microparticles were placed in a collagen gel, the cells quickly migrated off the microparticles and through the gel. Cells from seeded microparticles migrated to and across an in vitro anastomosis model, increasing the tensile strength of the model. Cell seeded microparticles of ECM material have potential for paracrine and cellular delivery therapies when delivered in a gel carrier. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1728-1735, 2016. PMID:26946064

  7. Driver’s Awareness and Lane Changing Maneuver in Traffic Flow based on Cellular Automaton Model

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2015-08-01

    Full Text Available Effect of driver’s awareness (e.g., to estimate the speed and arrival time of another vehicle on the lane changing maneuver is discussed. “Scope awareness” is defined as the visibility which is required for the driver to make a visual perception about road condition and the speed of vehicle that appears in the target lane for lane changing in the road. Cellular automaton based simulation model is created and applied to simulation studies for driver awareness behavior. This study clarifies relations between the lane changing behavior and the scope awareness parameter that reflects driver behavior. Simulation results show that the proposed model is valid for investigation of the important features of lane changing maneuver.

  8. Genome editing of human pluripotent stem cells to generate human cellular disease models

    Directory of Open Access Journals (Sweden)

    Kiran Musunuru

    2013-07-01

    Full Text Available Disease modeling with human pluripotent stem cells has come into the public spotlight with the awarding of the Nobel Prize in Physiology or Medicine for 2012 to Drs John Gurdon and Shinya Yamanaka for the discovery that mature cells can be reprogrammed to become pluripotent. This discovery has opened the door for the generation of pluripotent stem cells from individuals with disease and the differentiation of these cells into somatic cell types for the study of disease pathophysiology. The emergence of genome-editing technology over the past few years has made it feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Here, recent technological advances in genome editing, and its utility in human biology and disease studies, are reviewed.

  9. An improved cellular automaton model considering the effect of traffic lights and driving behaviour

    Science.gov (United States)

    He, Hong-Di; Lu, Wei-Zhen; Dong, Li-Yun

    2011-04-01

    This paper proposes an improved cellular automaton model to describe the urban traffic flow with the consideration of traffic light and driving behaviour effects. Based on the model, the characteristics of the urban traffic flow on a single-lane road are investigated under three different control strategies, i.e., the synchronized, the green wave and the random strategies. The fundamental diagrams and time-space patterns of the traffic flows are provided for these strategies respectively. It finds that the dynamical transition to the congested flow appears when the vehicle density is higher than a critical level. The saturated flow is less dependent on the cycle time and the strategies of the traffic light control, while the critical vehicle density varies with the cycle time and the strategies. Simulated results indicate that the green wave strategy is proven to be the most effective one among the above three control strategies.

  10. The Aldous-Shields model revisited (with application to cellular ageing)

    CERN Document Server

    Best, Katharina

    2010-01-01

    In Aldous and Shields (1988), a model for a rooted, growing random binary tree was presented. For some c>0, an external vertex splits at rate c^(-i) (and becomes internal) if its distance from the root (depth) is i. For c>1, we reanalyse the tree profile, i.e. the numbers of external vertices in depth i=1,2,.... Our main result are concrete formulas for the expectation and covariance-structure of the profile. In addition, we present the application of the model to cellular ageing. Here, we assume that nodes in depth h+1 are senescent, i.e. do not split. We obtain a limit result for the proportion of non-senescent vertices for large h.

  11. A cellular automation model for the change of public attitude regarding nuclear energy

    International Nuclear Information System (INIS)

    A cellular automation model was constructed to investigate how public opinion on nuclear energy in Japan depends upon the information environment and personal communication between people. From simulation with this model, the following become clear; (i) society is a highly non-linear system with a self-organizing potential: (ii) in a society composed of one type of constituent member with homogeneous characteristics, the trend of public opinion is substantially changed only when the effort to ameliorate public acceptance over a long period of time, by means such as education, persuasion and advertisement, exceeds a certain threshold, and (iii) in the case when the amount of information on nuclear risk released from the newsmedia is reduced continuously from now on, the acceptability of nuclear energy is significantly improved so far as the extent of the reduction exceeds a certain threshold. (author)

  12. DYNAMIC AND REALTIME MODELLING OF UBIQUITOUS INTERACTION

    Directory of Open Access Journals (Sweden)

    Imen Ismail

    2016-02-01

    Full Text Available Ubiquitous systems require user to be dynamically and realtime informed in order to make his current activity increasingly easy. First, this paper presents and discusses a method to model the realtime interaction of the user with a ubiquitous system based on Petri-nets modelling technology. The goal deals with investigating dynamically the appropriate form of interaction depending on the context of the user. Thus, the interaction model structure should be dynamically improved with respect to the current and particular activity or goal of the user to better cope with his runtime requirements. This mechanism has been characterized as “models mutation”. Secondly, this paper proves the dynamic construction of models while basing on the dynamic composition of services. The ultimate purpose is to take advantage of the ontology of service written in OWL-S in order to describe the dynamic aspect of Petri-nets based models, especially, the realtime and automatic composition of such models. Simulation work has been conducted to validate the proposed approach.

  13. Continuous macroscopic limit of a discrete stochastic model for interaction of living cells

    CERN Document Server

    Alber, M; Lushnikov, P M; Newman, S A; Alber, Mark; Chen, Nan; Lushnikov, Pavel M.; Newman, Stuart A.

    2007-01-01

    In the development of multiscale biological models it is crucial to establish a connection between discrete microscopic or mesoscopic stochastic models and macroscopic continuous descriptions based on cellular density. In this paper a continuous limit of a two-dimensional Cellular Potts Model (CPM) with excluded volume is derived, describing cells moving in a medium and reacting to each other through both direct contact and long range chemotaxis. The continuous macroscopic model is obtained as a Fokker-Planck equation describing evolution of the cell probability density function. All coefficients of the general macroscopic model are derived from parameters of the CPM and a very good agreement is demonstrated between CPM Monte Carlo simulations and numerical solution of the macroscopic model. It is also shown that in the absence of contact cell-cell interactions, the obtained model reduces to the classical macroscopic Keller-Segel model. General multiscale approach is demonstrated by simulating spongy bone for...

  14. Binary Particle Model of Weak Interactions

    CERN Document Server

    Ndili, F N

    2011-01-01

    We introduce the new concept of binary particle as the basic matter unit that participates in weak interactions and not any one fermion singly. We state the quantum numbers of this binary particle, and show the concept leads us to a natural explanation of the standard model puzzle of the origin of flavor mixing and the CKM matrix. Certain other puzzles of the standard model such as the absence of flavor changing neutral currents (FCNC), are also explained naturally by the binary particle model. These puzzles are currently thought to be esoteric properties of electro weak interactions that have origins in physics beyond the standard model at some ultra high energy scales. We show that this is not necessarily the case.

  15. Constraining dark energy interacting models with WMAP

    CERN Document Server

    Olivares, G; Pavón, D; Olivares, German; Atrio-Barandela, Fernando; Pavon, Diego

    2006-01-01

    We determine the range of parameter space of an interacting quintessence (IQ) model that best fits the luminosity distance of type Ia supernovae data and the recent WMAP measurements of Cosmic Microwave Background temperature anisotropies. Models in which quintessence decays into dark matter provide a clean explanation for the coincidence problem. We focus on cosmological models of zero spatial curvature. We show that if the dark energy (DE) decays into cold dark matter (CDM) at a rate that brings the ratio of matter to dark energy constant at late times, the supernovae data are not sufficient to constrain the interaction parameter. On the contrary, WMAP data constrain it to be smaller than $c^2 < 10^{-2}$ at the $3\\sigma$ level. Accurate measurements of the Hubble constant and the dark energy density, independent of the CMB data, would support/disprove this set of models.

  16. Unified models of electromagnetic and weak interactions

    International Nuclear Information System (INIS)

    After a brief summary of our knowledge on weak interactions the total weak neutral current is considered under the assumptions that neutral currents are of vector nature and the hadronic parts can be constructed out of quarks. The study of actual gauge models is started with the Salam-Weinberg model and extented by the Higgs field to circumvent the mass problem of intermediate bosons. The problem of no neutral strangeness changing transitions is discussed using charm and color. (BJ)

  17. Inverse Modeling of Cloud – Aerosol Interactions

    OpenAIRE

    Partridge, Daniel

    2011-01-01

    The role of aerosols and clouds is one of the largest sources of uncertainty in understanding climate change. The primary scientific goal of this thesis is to improve the understanding of cloud-aerosol interactions by applying inverse modeling using Markov Chain Monte Carlo (MCMC) simulation. Through a set of synthetic tests using a pseudo-adiabatic cloud parcel model, it is shown that a self adaptive MCMC algorithm can efficiently find the correct optimal values of meteorological and aerosol...

  18. ISAM - an Interactive Service for Asteroid Models

    Science.gov (United States)

    Bartczak, P.; Marciniak, A.

    2011-10-01

    We present an interactive web service for past and future physical ephemeris of polyhedral asteroid shape models obtained mainly with the lightcurve inversion method. Our tool allows for plane-of-sky views of the models, that can be then compared with asteroid images obtained using different techniques like occultations, radar or thermal infrared. Additionally, lightcurves, animated views, and stereoscopic images can be generated by the users. The service is available at the address: http://isam.astro.amu.edu.pl

  19. Preliminary definition of CORTEX interaction model

    OpenAIRE

    Biegel, G.; Brudna, C.; Casimiro, António; Kaiser, J; C. Liu; Mitidieri, C.; Veríssimo, Paulo

    2003-01-01

    As scheduled in the Technical Annex, WP2-D3 comprises work on the basic communication abstractions and the context and environmental awareness. It is structured in an introduction, providing a short survey of the content and four technical chapters. Chapter 2 describes the notion of event channels as a basic middleware abstraction of the interaction model. The concept of event channels accommodates an event-based, generative, many-to-many, anonymous communication model. It contributes to the ...

  20. Interaction of papaverine with model membranes

    International Nuclear Information System (INIS)

    The binding of the vasodilator drug papaverine (PAV) to model membranes was studied. Micelles of zwitterionic N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS) in D2 O were chosen as a model of lipid aggregates, while HPS fragments, cationic cetyltrimethylamonium chloride (CTAC) and anionic sodium dodecylsulfate (SDS) were used for studying the interaction of drugs with different parts of the polar HPS headgroup separately

  1. A nanoflare based cellular automaton model and the observed properties of the coronal plasma

    CERN Document Server

    Fuentes, Marcelo López

    2016-01-01

    We use the cellular automaton model described in L\\'opez Fuentes \\& Klimchuk (2015, ApJ, 799, 128) to study the evolution of coronal loop plasmas. The model, based on the idea of a critical misalignment angle in tangled magnetic fields, produces nanoflares of varying frequency with respect to the plasma cooling time. We compare the results of the model with active region (AR) observations obtained with the Hinode/XRT and SDO/AIA instruments. The comparison is based on the statistical properties of synthetic and observed loop lightcurves. Our results show that the model reproduces the main observational characteristics of the evolution of the plasma in AR coronal loops. The typical intensity fluctuations have an amplitude of 10 to 15\\% both for the model and the observations. The sign of the skewness of the intensity distributions indicates the presence of cooling plasma in the loops. We also study the emission measure (EM) distribution predicted by the model and obtain slopes in log(EM) versus log(T) betw...

  2. CellLab-CTS 2015: continuous-time stochastic cellular automaton modeling using Landlab

    Science.gov (United States)

    Tucker, Gregory E.; Hobley, Daniel E. J.; Hutton, Eric; Gasparini, Nicole M.; Istanbulluoglu, Erkan; Adams, Jordan M.; Siddartha Nudurupati, Sai

    2016-02-01

    CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS models. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.

  3. Modelling urban growth in the Indo-Gangetic plain using nighttime OLS data and cellular automata

    Science.gov (United States)

    Roy Chowdhury, P. K.; Maithani, Sandeep

    2014-12-01

    The present study demonstrates the applicability of the Operational Linescan System (OLS) sensor in modelling urban growth at regional level. The nighttime OLS data provides an easy, inexpensive way to map urban areas at a regional scale, requiring a very small volume of data. A cellular automata (CA) model was developed for simulating urban growth in the Indo-Gangetic plain; using OLS data derived maps as input. In the proposed CA model, urban growth was expressed in terms of causative factors like economy, topography, accessibility and urban infrastructure. The model was calibrated and validated based on OLS data of year 2003 and 2008 respectively using spatial metrics measures and subsequently the urban growth was predicted for the year 2020. The model predicted high urban growth in North Western part of the study area, in south eastern part growth would be concentrated around two cities, Kolkata and Howrah. While in the middle portion of the study area, i.e., Jharkhand, Bihar and Eastern Uttar Pradesh, urban growth has been predicted in form of clusters, mostly around the present big cities. These results will not only provide an input to urban planning but can also be utilized in hydrological and ecological modelling which require an estimate of future built up areas especially at regional level.

  4. Open boundaries in a cellular automaton model for traffic flow with metastable states

    Science.gov (United States)

    Barlovic, Robert; Huisinga, Torsten; Schadschneider, Andreas; Schreckenberg, Michael

    2002-10-01

    The effects of open boundaries in the velocity-dependent randomization (VDR) model, a modified version of the well-known Nagel-Schreckenberg (NaSch) cellular automaton model for traffic flow, are investigated. In contrast to the NaSch model, the VDR model exhibits metastable states and phase separation in a certain density regime. A proper insertion strategy allows us to investigate the whole spectrum of possible system states and the structure of the phase diagram by Monte Carlo simulations. We observe an interesting microscopic structure of the jammed phases, which is different from the one of the NaSch model. For finite systems, the existence of high flow states in a certain parameter regime leads to a special structure of the fundamental diagram measured in the open system. Apart from that, the results are in agreement with an extremal principle for the flow, which has been introduced for models with a unique flow-density relation. Finally, we discuss the application of our findings for a systematic flow optimization. Here some surprising results are obtained, e.g., a restriction of the inflow can lead to an improvement of the total flow through a bottleneck.

  5. (spdf) interacting boson model and its application

    International Nuclear Information System (INIS)

    The group structure and the general form of Hamiltonian of (spdf) interaction boson model are discussed. The energy spectra and the E1,E2 and E3 transition rates of 144Ba and 152Sm are calculated. The results agree with the experimental data quite well

  6. QSO evolution in the interaction model

    Energy Technology Data Exchange (ETDEWEB)

    De Robertis, M.

    1985-06-01

    QSO evolution is investigated according to the interaction hypothesis described most recently by Stockton (1982), in which activity results from an interaction between two galaxies resulting in the transfer of gas onto a supermassive black hole (SBH) at the center of at least one participant. Explicit models presented here for interactions in cluster environments show that a peak QSO population can be formed in this way at zroughly-equal2--3, with little activity prior to this epoch. Calculated space densities match those inferred from observations for this epoch. Substantial density evolution is expected in such models, since, after virialization, conditions in the cores of rich clusters lead to the depletion of gas-rich systems through ram-pressure stripping. Density evolution parameters of 6--12 are easily accounted for. At smaller redshifts, however, QSOs should be found primarily in poor clusters or groups. Probability estimates provided by this model are consistent with local estimates for the observed number of QSOs per interaction. Significant luminosity-dependent evolution might also be expected in these models. It is suggested that the mean SBH mass increases with lookback time, leading to a statistical brightening with redshift. Undoubtedly, both forms of evolution contribute to the overall QSO luminosity function.

  7. QSO evolution in the interaction model

    International Nuclear Information System (INIS)

    QSO evolution is investigated according to the interaction hypothesis described most recently by Stockton (1982), in which activity results from an interaction between two galaxies resulting in the transfer of gas onto a supermassive black hole (SBH) at the center of at least one participant. Explicit models presented here for interactions in cluster environments show that a peak QSO population can be formed in this way at zroughly-equal2--3, with little activity prior to this epoch. Calculated space densities match those inferred from observations for this epoch. Substantial density evolution is expected in such models, since, after virialization, conditions in the cores of rich clusters lead to the depletion of gas-rich systems through ram-pressure stripping. Density evolution parameters of 6--12 are easily accounted for. At smaller redshifts, however, QSOs should be found primarily in poor clusters or groups. Probability estimates provided by this model are consistent with local estimates for the observed number of QSOs per interaction. Significant luminosity-dependent evolution might also be expected in these models. It is suggested that the mean SBH mass increases with lookback time, leading to a statistical brightening with redshift. Undoubtedly, both forms of evolution contribute to the overall QSO luminosity function

  8. Intuitionistic preference modeling and interactive decision making

    CERN Document Server

    Xu, Zeshui

    2014-01-01

    This book offers an in-depth and comprehensive introduction to the priority methods of intuitionistic preference relations, the consistency and consensus improving procedures for intuitionistic preference relations, the approaches to group decision making based on intuitionistic preference relations, the approaches and models for interactive decision making with intuitionistic fuzzy information, and the extended results in interval-valued intuitionistic fuzzy environments.

  9. An equilibrium approach to modelling social interaction

    CERN Document Server

    Gallo, Ignacio

    2009-01-01

    The aim of this work is to put forward a statistical mechanics theory of social interaction, generalizing econometric discrete choice models. After showing the formal equivalence linking econometric multinomial logit models to equilibrium statical mechanics, a multi-population generalization of the Curie-Weiss model for ferromagnets is considered as a starting point in developing a model capable of describing sudden shifts in aggregate human behaviour. Existence of the thermodynamic limit for the model is shown by an asymptotic sub-additivity method and factorization of correlation functions is proved almost everywhere. The exact solution of the model is provided in the thermodynamical limit by finding converging upper and lower bounds for the system's pressure, and the solution is used to prove an analytic result regarding the number of possible equilibrium states of a two-population system. The work stresses the importance of linking regimes predicted by the model to real phenomena, and to this end it propo...

  10. Two-Photon Enzymatic Probes Visualizing Sub-cellular/Deep-brain Caspase Activities in Neurodegenerative Models.

    Science.gov (United States)

    Qian, Linghui; Zhang, Cheng-Wu; Mao, Yanli; Li, Lin; Gao, Nengyue; Lim, Kah-Leong; Xu, Qing-Hua; Yao, Shao Q

    2016-01-01

    Caspases work as a double-edged sword in maintaining cell homeostasis. Highly regulated caspase activities are essential during animal development, but dysregulation might lead to different diseases, e.g. extreme caspase activation is known to promote neurodegeneration. At present, visualization of caspase activation has mostly remained at the cellular level, in part due to a lack of cell-permeable imaging probes capable of direct, real-time investigations of endogenous caspase activities in deep tissues. Herein, we report a suite of two-photon, small molecule/peptide probes which enable sensitive and dynamic imaging of individual caspase activities in neurodegenerative models under physiological conditions. With no apparent toxicity and the ability of imaging endogenous caspases both in different subcellular organelles of mammalian cells and in brain tissues, these probes serve as complementary tools to conventional histological analysis. They should facilitate future explorations of caspases at molecular, cellular and organism levels and inspire development of novel two-photon probes against other enzymes. PMID:27210613

  11. Distinctive behavioral and cellular responses to fluoxetine in the mouse model for Fragile X syndrome

    Directory of Open Access Journals (Sweden)

    Marko eUutela

    2014-05-01

    Full Text Available Fluoxetine is used as a therapeutic agent for autism spectrum disorder (ASD, including Fragile X syndrome (FXS. The treatment often associates with disruptive behaviors such as agitation and disinhibited behaviors in FXS. To identify mechanisms that increase the risk to poor treatment outcome, we investigated the behavioral and cellular effects of fluoxetine on adult Fmr1 knockout (KO mice, a mouse model for FXS. We found that fluoxetine reduced anxiety-like behavior of both wild type and Fmr1 KO mice seen as shortened latency to enter the center area in the open field test. In Fmr1 KO mice, fluoxetine normalized locomotor hyperactivity but abnormally increased exploratory activity. Reduced Brain-derived neurotrophic factor (BDNF and increased TrkB receptor expression levels in the hippocampus of Fmr1 KO mice associated with inappropriate coping responses under stressful condition and abolished antidepressant activity of fluoxetine. Fluoxetine response in the cell proliferation was also missing in the hippocampus of Fmr1 KO mice when compared with wild type controls. The postnatal expression of serotonin transporter was reduced in the thalamic nuclei of Fmr1 KO mice during the time of transient innervation of somatosensory neurons suggesting that developmental changes of serotonin transporter (SERT expression were involved in the differential cellular and behavioral responses to fluoxetine in wild type and Fmr1 mice. The results indicate that changes of BDNF/TrkB signaling contribute to differential behavioral responses to fluoxetine among individuals with ASD.

  12. The influence of receptor-mediated interactions on reaction-diffusion mechanisms of cellular self-organisation.

    Science.gov (United States)

    Klika, Václav; Baker, Ruth E; Headon, Denis; Gaffney, Eamonn A

    2012-04-01

    Understanding the mechanisms governing and regulating self-organisation in the developing embryo is a key challenge that has puzzled and fascinated scientists for decades. Since its conception in 1952 the Turing model has been a paradigm for pattern formation, motivating numerous theoretical and experimental studies, though its verification at the molecular level in biological systems has remained elusive. In this work, we consider the influence of receptor-mediated dynamics within the framework of Turing models, showing how non-diffusing species impact the conditions for the emergence of self-organisation. We illustrate our results within the framework of hair follicle pre-patterning, showing how receptor interaction structures can be constrained by the requirement for patterning, without the need for detailed knowledge of the network dynamics. Finally, in the light of our results, we discuss the ability of such systems to pattern outside the classical limits of the Turing model, and the inherent dangers involved in model reduction. PMID:22072186

  13. Cognitive and Energy Harvesting-Based D2D Communication in Cellular Networks: Stochastic Geometry Modeling and Analysis

    OpenAIRE

    Sakr, Ahmed Hamdi; Hossain, Ekram

    2014-01-01

    While cognitive radio enables spectrum-efficient wireless communication, radio frequency (RF) energy harvesting from ambient interference is an enabler for energy-efficient wireless communication. In this paper, we model and analyze cognitive and energy harvesting-based D2D communication in cellular networks. The cognitive D2D transmitters harvest energy from ambient interference and use one of the channels allocated to cellular users (in uplink or downlink), which is referred to as the D2D c...

  14. Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction

    OpenAIRE

    Cheng, Y; Kekenes-Huskey, P; Hake, JE; Holst, MJ; McCammon, JA; Michailova, AP

    2012-01-01

    This article provides a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally-validated estimates ...

  15. Developing an Abaqus *HYPERFOAM Model for M9747 (4003047) Cellular Silicone Foam

    Energy Technology Data Exchange (ETDEWEB)

    Siranosian, Antranik A. [Los Alamos National Laboratory; Stevens, R. Robert [Los Alamos National Laboratory

    2012-04-26

    This report documents work done to develop an Abaqus *HYPERFOAM hyperelastic model for M9747 (4003047) cellular silicone foam for use in quasi-static analyses at ambient temperature. Experimental data, from acceptance tests for 'Pad A' conducted at the Kansas City Plant (KCP), was used to calibrate the model. The data includes gap (relative displacement) and load measurements from three locations on the pad. Thirteen sets of data, from pads with different serial numbers, were provided. The thirty-nine gap-load curves were extracted from the thirteen supplied Excel spreadsheets and analyzed, and from those thirty-nine one set of data, representing a qualitative mean, was chosen to calibrate the model. The data was converted from gap and load to nominal (engineering) strain and nominal stress in order to implement it in Abaqus. Strain computations required initial pad thickness estimates. An Abaqus model of a right-circular cylinder was used to evaluate and calibrate the *HYPERFOAM model.

  16. Scaling, phase transitions, and nonuniversality in a self-organized critical cellular-automaton model

    International Nuclear Information System (INIS)

    We present a two-dimensional continuous cellular automaton that is equivalent to a driven spring-block model. Both the conservation and the anisotropy in the model are controllable quantities. Above a critical level of conservation, the model exhibits self-organized criticality. The self-organization of this system and hence the critical exponents depend on the conservation and the boundary conditions. In the critical isotropic nonconservative phase, the exponents change continuously as a function of conservation. Furthermore, the exponents vary continuously when changing the boundary conditions smoothly. Consequently, there is no universality of the critical exponents. We discuss the relevance of this for earthquakes. Introducing anisotropy changes the scaling of the distribution function, but not the power-law exponent. We explore the phase diagram of this model. We find that at low conservation levels a localization transition occurs. We see two additional phase transitions. The first is seen when moving from the conservative into the nonconservative model. The second appears when passing from the anisotropic two-dimensional system to the purely one-dimensional system

  17. Derivation of Solar Flare Cellular Automata Models from a Subset of the Magnetohydrodynamic Equations

    Science.gov (United States)

    Vassiliadis, D.; Anastasiadis, A.; Georgoulis, M.; Vlahos, L.

    1998-12-01

    Cellular automata (CA) models account for the power-law distributions found for solar flare hard X-ray observations, but their physics has been unclear. We examine four of these models and show that their criteria and magnetic field distribution rules can be derived by discretizing the MHD diffusion equation as obtained from a simplified Ohm's law. Identifying the discrete MHD with the CA models leads to an expression for the resistivity as a function of the current on the flux tube boundary, as may be expected from current-driven instabilities. Anisotropic CA models correspond to a nonlinear resistivity η(J), while isotropic ones are associated with hyperresistivity η(▽2J). The discrete equations satisfy the necessary conditions for self-organized criticality (Lu): there is local conservation of a field (magnetic flux), while the nonlinear resistivity provides a rapid dissipation and relaxation mechanism. The approach justifies many features of the CA models that were originally based on intuition.

  18. A multi-objective model for designing a group layout of a dynamic cellular manufacturing system

    Science.gov (United States)

    Kia, Reza; Shirazi, Hossein; Javadian, Nikbakhsh; Tavakkoli-Moghaddam, Reza

    2013-04-01

    This paper presents a multi-objective mixed-integer nonlinear programming model to design a group layout of a cellular manufacturing system in a dynamic environment, in which the number of cells to be formed is variable. Cell formation (CF) and group layout (GL) are concurrently made in a dynamic environment by the integrated model, which incorporates with an extensive coverage of important manufacturing features used in the design of CMSs. Additionally, there are some features that make the presented model different from the previous studies. These features include the following: (1) the variable number of cells, (2) the integrated CF and GL decisions in a dynamic environment by a multi-objective mathematical model, and (3) two conflicting objectives that minimize the total costs (i.e., costs of intra and inter-cell material handling, machine relocation, purchasing new machines, machine overhead, machine processing, and forming cells) and minimize the imbalance of workload among cells. Furthermore, the presented model considers some limitations, such as machine capability, machine capacity, part demands satisfaction, cell size, material flow conservation, and location assignment. Four numerical examples are solved by the GAMS software to illustrate the promising results obtained by the incorporated features.

  19. Mechanism of Laser/light beam interaction at cellular and tissue level and study of the influential factors for the application of low level laser therapy

    CERN Document Server

    Khalid, Muhammad Zeeshan

    2016-01-01

    After the discovery of laser therapy it was realized it has useful application of wound healing and reduce pain, but due to the poor understanding of the mechanism and dose response this technique remained to be controversial for therapeutic applications. In order to understand the working and effectiveness different experiments were performed to determine the laser beam effect at the cellular and tissue level. This article discusses the mechanism of beam interaction at tissues and cellular level with different light sources and dosimetry principles for clinical application of low level laser therapy. Different application techniques and methods currently in use for clinical treatment has also been reviewed.

  20. Direct interaction of cellular hnRNP-F and NS1 of influenza A virus accelerates viral replication by modulation of viral transcriptional activity and host gene expression

    International Nuclear Information System (INIS)

    To investigate novel NS1-interacting proteins, we conducted a yeast two-hybrid analysis, followed by co-immunoprecipitation assays. We identified heterogeneous nuclear ribonucleoprotein F (hnRNP-F) as a cellular protein interacting with NS1 during influenza A virus infection. Co-precipitation assays suggest that interaction between hnRNP-F and NS1 is a common and direct event among human or avian influenza viruses. NS1 and hnRNP-F co-localize in the nucleus of host cells, and the RNA-binding domain of NS1 directly interacts with the GY-rich region of hnRNP-F determined by GST pull-down assays with truncated proteins. Importantly, hnRNP-F expression levels in host cells indicate regulatory role on virus replication. hnRNP-F depletion by small interfering RNA (siRNA) shows 10- to 100-fold increases in virus titers corresponding to enhanced viral RNA polymerase activity. Our results delineate novel mechanism of action by which NS1 accelerates influenza virus replication by modulating normal cellular mRNA processes through direct interaction with cellular hnRNP-F protein.

  1. Hadronic interaction models and air shower simulations

    International Nuclear Information System (INIS)

    Extensive air showers can only be interpreted by comparison of the measured observables with simulations, using a suitable model for the shower development in the atmosphere. Due to the complexity of the phenomenon, in the past the models were quite simple and results from air showers were to interpret qualitatively, at best. With a new generation of experiments more advanced detectors became operational and the need for detailed simulations grew. In recent years several new air shower programs were developed. Using the rapid increase of the computing power they have now reached a high level of sophistication. Particle transport, electromagnetic interactions and decay of unstable particles are treated in great detail. However the most crucial ingredient to all these programs is the modeling of hadronic interactions since it requires extrapolation in energy, primary mass and kinematics to regions where no accelerator data exist and where theoretical guidelines are only vague. As a consequence of the model uncertainties, experiments using different models occasionally reached very different conclusions on energy spectra and composition of the cosmic rays. CORSIKA is an extensive air shower simulation program that contains five different hadronic interaction models (VENUS, QGSJET, SIBYLL, HDPM, and DPMJET). It is widely used throughout the cosmic ray community and allows the study of model dependencies and the systematic effects of measurement and event reconstruction. Results for different models concerning inelastic cross-sections and particle production and their influence on air shower variables are discussed and the systematic uncertainties for air shower analyses are investigated. The capability of precise multi-parameter measurements to discriminate between the models is emphasised

  2. Understanding and modelling man-machine interaction

    International Nuclear Information System (INIS)

    This paper gives an overview of the current state of the art in man-machine system interaction studies, focusing on the problems derived from highly automated working environments and the role of humans in the control loop. In particular, it is argued that there is a need for sound approaches to the design and analysis of man-machine interaction (MMI), which stem from the contribution of three expertises in interfacing domains, namely engineering, computer science and psychology: engineering for understanding and modelling plants and their material and energy conservation principles; psychology for understanding and modelling humans an their cognitive behaviours; computer science for converting models in sound simulations running in appropriate computer architectures. (orig.)

  3. Understanding and modelling Man-Machine Interaction

    International Nuclear Information System (INIS)

    This paper gives an overview of the current state of the art in man machine systems interaction studies, focusing on the problems derived from highly automated working environments and the role of humans in the control loop. In particular, it is argued that there is a need for sound approaches to design and analysis of Man-Machine Interaction (MMI), which stem from the contribution of three expertises in interfacing domains, namely engineering, computer science and psychology: engineering for understanding and modelling plants and their material and energy conservation principles; psychology for understanding and modelling humans and their cognitive behaviours; computer science for converting models in sound simulations running in appropriate computer architectures. (author)

  4. Algebraic Turbulence-Chemistry Interaction Model

    Science.gov (United States)

    Norris, Andrew T.

    2012-01-01

    The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

  5. "A Cellular Encounter": Constructing the Cell as a Whole System Using Illustrative Models

    Science.gov (United States)

    Cohen, Joel I.

    2014-01-01

    A standard part of biology curricula is a project-based assessment of cell structure and function. However, these are often individual assignments that promote little problem-solving or group learning and avoid the subject of organelle chemical interactions. I evaluate a model-based cell project designed to foster group and individual guided…

  6. An Option Pricing Model Based on Cellular Automaton%基于元胞自动机的期权定价模型

    Institute of Scientific and Technical Information of China (English)

    李捷

    2011-01-01

    Option pricing is one of the most difficult problems in financial research. The key to the problem is how to simulate the randomness of the underlying asset price. This paper designs and implements an option pricing model based on the cellular automaton, which treats market participants as the cells in the cellular automaton. The model uses cellular automaton rules to simulate the interactions between traders and the changes of underlying asset prices. The paper compares the output data of the model with the calculation results of the Black-Scholes model, tests the normality of the model's output data, and finds that the option pricing model based on the cellular automaton is not only feasible, but also more effective than the Black-Scholes model.%针对期权定价难于模拟基础资产价格波动随机性的问题,设计了基于元胞自动机的期权定价模型.该模型将市场参与者看作一个个的元胞,使用元胞规则来模拟金融市场中交易者之间的交互行为。从而在总体上模拟出基础资产价格的变化.比较了模型产出的数据和Black-Scholes模型的计算结果,检验了模型产出数据的正态性,发现基于元胞自动机的期权定价模型不仅具有可行性,而且比Black-Scholes模型更有效.

  7. Secret neutrino interactions: a pseudoscalar model

    Science.gov (United States)

    Archidiacono, Maria; Hannestad, Steen; Sloth Hansen, Rasmus; Tram, Thomas

    2016-05-01

    Neutrino oscillation experiments point towards the existence of additional mostly sterile neutrino mass eigenstates in the eV mass range. At the same time, such sterile neutrinos are disfavoured by cosmology (Big Bang Nucleosynthesis, Cosmic Microwave Background and Large Scale Structure), unless they can be prevented from being thermalised in the early Universe. To this aim, we introduce a model of sterile neutrino secret interactions mediated by a new light pseudoscalar: The new interactions can accomodate sterile neutrinos in the early Universe, providing a good fit to all the up to date cosmological data.

  8. IPPI-model of hadron interactions

    CERN Document Server

    Dremin, I M

    2004-01-01

    A model of Independent Pair Parton Interactions (IPPI) is proposed. According to it, hadron interactions are represented by a set of independent binary parton collisions. The final multiplicity distribution is described by a convolution of the negative binomial distributions in each of the partonic collisions. As a result, it is given by a weighted sum of negative binomial distributions with parameters multiplied by the number of active pairs. Its shape and moments are considered. Experimental data on multiplicity distributions in high energy $p\\bar p$ processes are well fitted by these distributions. Predictions for LHC and higher energies are presented. Difference between $e^+e^-$ and $p\\bar p$ is discussed.

  9. Non-commutative model of quark interactions

    International Nuclear Information System (INIS)

    A non-commutative model of quark interactions with the generalized O(2.6) symmetry in quantum phase space is considered. The model is based on the Snyder-Yang algebra, which includes in the relativistically invariant way two parameters μc and λc with dimensionality of mass and length. The equations of motion obtained in the framework of the model contain the rising potentials which provide the confinement of color particles. The values of the parameters μc and λc, as well as the masses of constituent and current quarks are estimated

  10. Molecular modeling of the conformational dynamics of the cellular prion protein

    Science.gov (United States)

    Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

    2014-03-01

    Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

  11. Fatigue design of a cellular phone folder using regression model-based multi-objective optimization

    Science.gov (United States)

    Kim, Young Gyun; Lee, Jongsoo

    2016-08-01

    In a folding cellular phone, the folding device is repeatedly opened and closed by the user, which eventually results in fatigue damage, particularly to the front of the folder. Hence, it is important to improve the safety and endurance of the folder while also reducing its weight. This article presents an optimal design for the folder front that maximizes its fatigue endurance while minimizing its thickness. Design data for analysis and optimization were obtained experimentally using a test jig. Multi-objective optimization was carried out using a nonlinear regression model. Three regression methods were employed: back-propagation neural networks, logistic regression and support vector machines. The AdaBoost ensemble technique was also used to improve the approximation. Two-objective Pareto-optimal solutions were identified using the non-dominated sorting genetic algorithm (NSGA-II). Finally, a numerically optimized solution was validated against experimental product data, in terms of both fatigue endurance and thickness index.

  12. Phase transition in the economically modeled growth of a cellular nervous system

    CERN Document Server

    Nicosia, Vincenzo; Schafer, William R; Latora, Vito; Bullmore, Edward T; 10.1073/pnas.1300753110

    2013-01-01

    Spatially-embedded complex networks, such as nervous systems, the Internet and transportation networks, generally have non-trivial topological patterns of connections combined with nearly minimal wiring costs. However the growth rules shaping these economical trade-offs between cost and topology are not well understood. Here we study the cellular nervous system of the nematode worm C. elegans, together with information on the birth times of neurons and on their spatial locations. We find that the growth of this network undergoes a transition from an accelerated to a constant increase in the number of links (synaptic connections) as a function of the number of nodes (neurons). The time of this phase transition coincides closely with the observed moment of hatching, when development switches metamorphically from oval to larval stages. We use graph analysis and generative modelling to show that the transition between different growth regimes, as well as its coincidence with the moment of hatching, can be explain...

  13. Phase transitions in a cellular automaton model of a highway on-ramp

    Science.gov (United States)

    Belitsky, Vladimir; Maric, Nevena; Schütz, Gunter M.

    2007-09-01

    We introduce a lattice gas model for the merging of two single-lane automobile highways. The merging rules for traffic on the two lanes are deterministic, but the inflow on both lanes is stochastic. Analysing the stationary distribution of this stochastic cellular automaton, we find a discontinuous phase transition from a free-flow phase which depends on the initial state of the road to a jammed phase where all memory of the initial state is lost. Inside the jammed phase we identify dynamical phase transitions in the approach to stationarity. Each dynamical phase is characterized by a fixed number of relaxation cycles which is decreasing as one moves deeper into the jammed phase. In each cycle step, the number of 'desperate' drivers who force their way onto the main road when they reach the end of the on-ramp increases until stationarity.

  14. Phase transitions in a cellular automaton model of a highway on-ramp

    International Nuclear Information System (INIS)

    We introduce a lattice gas model for the merging of two single-lane automobile highways. The merging rules for traffic on the two lanes are deterministic, but the inflow on both lanes is stochastic. Analysing the stationary distribution of this stochastic cellular automaton, we find a discontinuous phase transition from a free-flow phase which depends on the initial state of the road to a jammed phase where all memory of the initial state is lost. Inside the jammed phase we identify dynamical phase transitions in the approach to stationarity. Each dynamical phase is characterized by a fixed number of relaxation cycles which is decreasing as one moves deeper into the jammed phase. In each cycle step, the number of 'desperate' drivers who force their way onto the main road when they reach the end of the on-ramp increases until stationarity

  15. Cellular and circuit models of increased resting-state network gamma activity in schizophrenia.

    Science.gov (United States)

    White, R S; Siegel, S J

    2016-05-01

    Schizophrenia (SCZ) is a disorder characterized by positive symptoms (hallucinations, delusions), negative symptoms (blunted affect, alogia, reduced sociability, and anhedonia), as well as persistent cognitive deficits (memory, concentration, and learning). While the biology underlying subjective experiences is difficult to study, abnormalities in electroencephalographic (EEG) measures offer a means to dissect potential circuit and cellular changes in brain function. EEG is indispensable for studying cerebral information processing due to the introduction of techniques for the decomposition of event-related activity into its frequency components. Specifically, brain activity in the gamma frequency range (30-80Hz) is thought to underlie cognitive function and may be used as an endophenotype to aid in diagnosis and treatment of SCZ. In this review we address evidence indicating that there is increased resting-state gamma power in SCZ. We address how modeling this aspect of the illness in animals may help treatment development as well as providing insights into the etiology of SCZ. PMID:26577758

  16. A Discrete/continuous Coupled Approach for Modeling Impacts on Cellular Geostructures

    Science.gov (United States)

    Breugnot, A.; Lambert, S.; Villard, P.; Gotteland, P.

    2016-05-01

    This article presents a numerical model coupling the finite difference method and discrete element methods (FDM, DEM) for simulating the response of cellular geostructures to impacts. DEM is used in the vicinity of the impacted area while FDM is used far away. The continuity between the DEM and FDM domains is insured using the edge-to-edge method. The numerical parameters are calibrated based on compression and impact experiments conducted on elementary cells. Numerical simulations at the structure scale are compared with real-scale experimental data. The response of the structure is addressed varying the impact conditions. The projectile shape and the position of the impact point appear to be the most influential parameters.

  17. Cellular Automata Models of Traffic Behavior in Presence of Speed Breaking Structures

    International Nuclear Information System (INIS)

    In this article, we study traffic flow in the presence of speed breaking structures. The speed breakers are typically used to reduce the local speed of vehicles near certain institutions such as schools and hospitals. Through a cellular automata model we study the impact of such structures on global traffic characteristics. The simulation results indicate that the presence of speed breakers could reduce the global flow under moderate global densities. However, under low and high global density traffic regime the presence of speed breakers does not have an impact on the global flow. Further the speed limit enforced by the speed breaker creates a phase distinction. For a given global density and slowdown probability, as the speed limit enforced by the speed breaker increases, the traffic moves from the reduced flow phase to maximum flow phase. This underlines the importance of proper design of these structures to avoid undesired flow restrictions. (general)

  18. Neuroprotective effects of protocatechuic aldehyde against neurotoxin-induced cellular and animal models of Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Xin Zhao

    Full Text Available Protocatechuic aldehyde (PAL has been reported to bind to DJ-1, a key protein involved in Parkinson's disease (PD, and exerts potential neuroprotective effects via DJ-1 in SH-SY5Y cells. In this study, we investigated the neuroprotective pharmacological effects of PAL against neurotoxin-induced cell and animal models of PD. In cellular models of PD, PAL markedly increased cell viability rates, mitochondrial oxidation-reduction activity and mitochondrial membrane potential, and reduced intracellular ROS levels to prevent neurotoxicity in PC12 cells. In animal models of PD, PAL reduced the apomorphine injection, caused turning in 6-OHDA treated rats, and increased the motor coordination and stride decreases in MPTP treated mice. Meanwhile, in an MPTP mouse model, PAL prevented a decrease of the contents of dopamine (DA and its metabolites in the striatum and TH-positive dopaminergic neuron loss in the substantia nigra (SN. In addition, PAL increased the protein expression of DJ-1 and reduced the level of α-synuclein in the SN of MPTP lesioned mice. PAL also increased the spine density in hippocampal CA1 neurons. The current study demonstrates that PAL can efficiently protect dopaminergic neurons against neurotoxin injury in vitro and in vivo, and that the potential mechanisms may be related to its effects in increasing DJ-1, decreasing α-synuclein and its growth-promoting effect on spine density.

  19. Lattice gas cellular automation model for rippling and aggregation in myxobacteria

    Science.gov (United States)

    Alber, Mark S.; Jiang, Yi; Kiskowski, Maria A.

    2004-05-01

    A lattice gas cellular automation (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2-3 min, a minimum response time of up to 1 min and no maximum oscillation period best reproduce rippling in the experiments of Myxococcus xanthus. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented.

  20. Cellular replication limits in the Luria-Delbrück mutation model

    Science.gov (United States)

    Rodriguez-Brenes, Ignacio A.; Wodarz, Dominik; Komarova, Natalia L.

    2016-08-01

    Originally developed to elucidate the mechanisms of natural selection in bacteria, the Luria-Delbrück model assumed that cells are intrinsically capable of dividing an unlimited number of times. This assumption however, is not true for human somatic cells which undergo replicative senescence. Replicative senescence is thought to act as a mechanism to protect against cancer and the escape from it is a rate-limiting step in cancer progression. Here we introduce a Luria-Delbrück model that explicitly takes into account cellular replication limits in the wild type cell population and models the emergence of mutants that escape replicative senescence. We present results on the mean, variance, distribution, and asymptotic behavior of the mutant population in terms of three classical formulations of the problem. More broadly the paper introduces the concept of incorporating replicative limits as part of the Luria-Delbrück mutational framework. Guidelines to extend the theory to include other types of mutations and possible applications to the modeling of telomere crisis and fluctuation analysis are also discussed.

  1. Stability Analysis of a Hybrid Cellular Automaton Model of Cell Colony Growth

    CERN Document Server

    Gerlee, P

    2007-01-01

    Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell colony growth. In the model the growth of the colony is limited by a nutrient that is consumed by the cells and which inhibits cell division if it falls below a certain threshold. Using this model we have investigated how the nutrient consumption rate of the cells affects the growth dynamics of the colony. We found that for low consumption rates the colony takes on a Eden-like morphology, while for higher consumption rates the morphology of the colony is branched with a fractal geometry. These findings are in agreement with previous results, but the simplicity of the model presented here allows for a linear stability analysis of the system. By observing that the local growth of the colony is proportional to the flux of the nutrient we derive an approximate dispersion relation fo...

  2. Large-scale parallel lattice Boltzmann-cellular automaton model of two-dimensional dendritic growth

    Science.gov (United States)

    Jelinek, Bohumir; Eshraghi, Mohsen; Felicelli, Sergio; Peters, John F.

    2014-03-01

    An extremely scalable lattice Boltzmann (LB)-cellular automaton (CA) model for simulations of two-dimensional (2D) dendritic solidification under forced convection is presented. The model incorporates effects of phase change, solute diffusion, melt convection, and heat transport. The LB model represents the diffusion, convection, and heat transfer phenomena. The dendrite growth is driven by a difference between actual and equilibrium liquid composition at the solid-liquid interface. The CA technique is deployed to track the new interface cells. The computer program was parallelized using the Message Passing Interface (MPI) technique. Parallel scaling of the algorithm was studied and major scalability bottlenecks were identified. Efficiency loss attributable to the high memory bandwidth requirement of the algorithm was observed when using multiple cores per processor. Parallel writing of the output variables of interest was implemented in the binary Hierarchical Data Format 5 (HDF5) to improve the output performance, and to simplify visualization. Calculations were carried out in single precision arithmetic without significant loss in accuracy, resulting in 50% reduction of memory and computational time requirements. The presented solidification model shows a very good scalability up to centimeter size domains, including more than ten million of dendrites. Catalogue identifier: AEQZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 29,767 No. of bytes in distributed program, including test data, etc.: 3131,367 Distribution format: tar.gz Programming language: Fortran 90. Computer: Linux PC and clusters. Operating system: Linux. Has the code been vectorized or parallelized?: Yes. Program is parallelized using MPI

  3. Motion Model Employment using interacting Motion Model Algorithm

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar

    2006-01-01

    The paper presents a simulation study to track a maneuvering target using a selective approach in choosing Interacting Multiple Models (IMM) algorithm to provide a wider coverage to track such targets.  Initially, there are two motion models in the system to track a target.  Probability of each m...

  4. Quantum cellular automata

    Science.gov (United States)

    Porod, Wolfgang; Lent, Craig S.; Bernstein, Gary H.

    1994-06-01

    The Notre Dame group has developed a new paradigm for ultra-dense and ultra-fast information processing in nanoelectronic systems. These Quantum Cellular Automata (QCA's) are the first concrete proposal for a technology based on arrays of coupled quantum dots. The basic building block of these cellular arrays is the Notre Dame Logic Cell, as it has been called in the literature. The phenomenon of Coulomb exclusion, which is a synergistic interplay of quantum confinement and Coulomb interaction, leads to a bistable behavior of each cell which makes possible their use in large-scale cellular arrays. The physical interaction between neighboring cells has been exploited to implement logic functions. New functionality may be achieved in this fashion, and the Notre Dame group invented a versatile majority logic gate. In a series of papers, the feasibility of QCA wires, wire crossing, inverters, and Boolean logic gates was demonstrated. A major finding is that all logic functions may be integrated in a hierarchial fashion which allows the design of complicated QCA structures. The most complicated system which was simulated to date is a one-bit full adder consisting of some 200 cells. In addition to exploring these new concepts, efforts are under way to physically realize such structures both in semiconductor and metal systems. Extensive modeling work of semiconductor quantum dot structures has helped identify optimum design parameters for QCA experimental implementations.

  5. Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model

    Directory of Open Access Journals (Sweden)

    Padilla-Longoria Pablo

    2008-11-01

    Full Text Available Abstract Background Dynamical models are instrumental for exploring the way information required to generate robust developmental patterns arises from complex interactions among genetic and non-genetic factors. We address this fundamental issue of developmental biology studying the leaf and root epidermis of Arabidopsis. We propose an experimentally-grounded model of gene regulatory networks (GRNs that are coupled by protein diffusion and comprise a meta-GRN implemented on cellularised domains. Results Steady states of the meta-GRN model correspond to gene expression profiles typical of hair and non-hair epidermal cells. The simulations also render spatial patterns that match the cellular arrangements observed in root and leaf epidermis. As in actual plants, such patterns are robust in the face of diverse perturbations. We validated the model by checking that it also reproduced the patterns of reported mutants. The meta-GRN model shows that interlinked sub-networks contribute redundantly to the formation of robust hair patterns and permits to advance novel and testable predictions regarding the effect of cell shape, signalling pathways and additional gene interactions affecting spatial cell-patterning. Conclusion The spatial meta-GRN model integrates available experimental data and contributes to further understanding of the Arabidopsis epidermal system. It also provides a systems biology framework to explore the interplay among sub-networks of a GRN, cell-to-cell communication, cell shape and domain traits, which could help understanding of general aspects of patterning processes. For instance, our model suggests that the information needed for cell fate determination emerges from dynamic processes that depend upon molecular components inside and outside differentiating cells, suggesting that the classical distinction of lineage versus positional cell differentiation may be instrumental but rather artificial. It also suggests that interlinkage

  6. Comments on interactions in the SUSY models

    CERN Document Server

    Upadhyay, Sudhakar; Mandal, Bhabani Prasad

    2016-01-01

    We consider the special supersymmetry (SUSY) transformations with $m$ generators $\\overleftarrow{s}_\\alpha,$ for some class of the models and study the physical consequences when making the Grassmann-odd transformations to form an Abelian supergroup with finite parameters and set of group-like elements with finite parameters being by a functionals of field variables. The SUSY-invariant path integral measure within conventional quantization scheme leads to appearance of the Jacobian under change of variables generated by such SUSY transformations, which is explicitly calculated. The Jacobian leads, first, to appearance of only trivial interactions in the transformed action, second, to the presence of modified Ward identity, which reduceds to the standard Ward identities for constant parameters. We examine the case of ${N}=1$, $N=2$ supersymmetric harmonic oscillator to illustrate the general concept on a free simple model with $(1,1)$ physical degrees of freedom. It is shown that the interaction terms, $U_{tr}...

  7. A trans-well-based cellular model for the rapid pre-evaluation of tympanic membrane repair materials.

    Science.gov (United States)

    Hung, Shih-Han; Su, Chin-Hui; Tseng, How

    2016-08-01

    It is important to have a standardized tympanic membrane (TM) perforation platform to evaluate the various myringoplasty materials that have been studied and developed extensively during recent years. However, currently there are no cellular models specifically designed for this purpose, and animal models remain unsatisfactory. The purpose of this study is to propose an inexpensive, readily available, well-controlled, and easy-to-create cellular model as a substitute for use in the evaluation of TM repairing materials. A trans-well model was created using a cell culture insert with a round hole created at the center of the polycarbonate membrane. HaCaT cells were cultured on the fenestrated culture insert, and the desired myringoplasty graft was placed at the center of the window for one week and observed by fluorescent microscopy under vital staining. Under this cellular model, there was notable migration of HaCaT cells onto the positive control graft (rabbit fascia), while only a few cell clusters were observed on the negative control graft (paper). Model validation showed that the cell migration ratio for the PLLA + 1% hyaluronic acid (HA) graft is significantly higher than using myringoplasty paper, poly L-lactide (PLLA), or PLLA + 0.5% HA (p < 0.05). This trans-well-based cellular model might be a useful pre-evaluation platform for the evaluation of TM repairing materials. The model is inexpensive, readily available, easy to create, and standardized for use. PMID:26335291

  8. Microscopic foundation of the interacting boson model

    International Nuclear Information System (INIS)

    A microscopic foundation of the interacting boson model is described. The importance of monopole and quadrupole pairs of nucleons is emphasized. Those pairs are mapped onto the s and d bosons. It is shown that this mapping provides a good approximation in vibrational and transitional nuclei. In appendix, it is shown that the monopole pair of electrons plays possibly an important role in metal clusters. (orig.)

  9. The Standard Model of Electroweak Interactions

    CERN Document Server

    Pich, Antonio

    2012-01-01

    Gauge invariance is a powerful tool to determine the dynamical forces among the fundamental constituents of matter. The particle content, structure and symmetries of the Standard Model Lagrangian are discussed. Special emphasis is given to the many phenomenological tests which have established this theoretical framework as the Standard Theory of the electroweak interactions: electroweak precision tests, Higgs searches, quark mixing, neutrino oscillations. The present experimental status is summarized.

  10. Modeling and boundary force control of microcantilevers utilized in atomic force microscopy for cellular imaging and characterization

    Science.gov (United States)

    Eslami, Sohrab

    This dissertation undertakes the theoretical and experimental developments microcantilevers utilized in Atomic Force Microscopy (AFM) with applications to cellular imaging and characterization. The capability of revealing the inhomogeneties or interior of ultra-small materials has been of most interest to many researchers. However, the fundamental concept of signal and image formation remains unexplored and not fully understood. For his, a semi-empirical nonlinear force model is proposed to show that virtual frequency generation, regarded as the simplest synthesized subsurface probe, occurs optimally when the force is tuned to the van der Waals form. This is the first-time observation of a novel theoretical dynamic multi-frequency force microscopy that has not been already reported. Owing to the broad applications of microcantilevers in the nanoscale imaging and microscopic techniques, there is an essential feeling to study and propose a comprehensive model of such systems. Therefore, in the theoretical part of this dissertation, a distributed-parameters representation modeling of the microcantilever along with a general interaction force comprising of two attractive and repulsive components with general amplitude and power terms is studied. This model is investigated in a general 2D Cartesian coordinate to consider the motions of the probe with a tip mass. There is an excitation at the microcantilever's base such that the end of the beam is subject to the proposed general force. These forces are very sensitive to the amplitude and power terms of these parts; on the other hand, atomic intermolecular force is a function of the distance such that this distance itself is also a function of the interaction force that will result in a nonlinear implicit equation. From a parametric study in the probe-sample excitation, it is shown that the predicted behavior of the generated difference-frequency oscillation amplitude agrees well with experimental measurements. Following

  11. Development of novel cellular model for affinity studies of histamine H(4) receptor ligands.

    Science.gov (United States)

    Karcz, Tadeusz; Kieć-Kononowicz, Katarzyna

    2013-01-01

    The G protein-coupled histamine H4 receptor (H4R) is the last member of histamine receptors family discovered so far. Its expression pattern, together with postulated involvement in a wide variety of immunological and inflammatory processes make histamine H4 receptor an interesting target for drug development. Potential H4R ligands may provide an innovative therapies for different immuno-based diseases, including allergy, asthma, pruritus associated with allergy or autoimmune skin conditions, rheumatoid arthritis and pain. However, none of successfully developed selective and potent histamine H4 receptor ligands have been introduced to the market up to date. For that reason there is still a strong demand for pharmacological models to be used in studies on potent H4R ligands. In current work we present the development of novel mammalian cell line, stably expressing human histamine H4 receptor, with use of retroviral transduction approach. Obtained cell line was pharmacologically characterized in radioligand binding studies and its utility for affinity testing of potent receptor ligands was confirmed in comparative studies with the use of relevant insect cells expression model. Obtained results allow for statement that developed cellular model may be successfully employed in search for new compounds active at histamine H4 receptor. PMID:24432340

  12. Effect of Driver Scope Awareness in the Lane Changing Maneuvers Using Cellular Automaton Model

    Directory of Open Access Journals (Sweden)

    Kohei Arai

    2013-07-01

    Full Text Available This paper investigated the effect of drivers’ visibility and their perception (e.g., to estimate the speed and arrival time of another vehicle on the lane changing maneuver. The term of scope awareness was used to describe the visibility required by the driver to make a perception about road condition and the speed of vehicle that exist in that road. A computer simulation model was conducted to show this driver awareness behavior. This studying attempt to precisely catching the lane changing behavior and illustrate the scope awareness parameter that reflects driver behavior. This paper proposes a simple cellular automata model for studying driver visibility effects of lane changing maneuver and driver perception of estimated speed. Different values of scope awareness were examined to capture its effect on the traffic flow. Simulation results show the ability of this model to capture the important features of lane changing maneuver and revealed the appearance of the short-thin solid line jam and the wide solid line jam in the traffic flow as the consequences of lane changing maneuver.

  13. An earthquake model with interacting asperities

    Science.gov (United States)

    Johnson, Lane R.

    2010-09-01

    A model is presented that treats an earthquake as the failure of asperities in a manner consistent with modern concepts of sliding friction. The mathematical description of the model includes results for elliptical and circular asperities, oblique tectonic slip, static and dynamic solutions for slip on the fault, stress intensity factors, strain energy and second-order moment tensor. The equations that control interaction of asperities are derived and solved both in a quasi-static tectonic mode when none of the asperities are in the process of failing and a dynamic failure mode when asperities are failing and sending out slip pulses that can trigger failure of additional asperities. The model produces moment rate functions for each asperity failure so that, given an appropriate Green function, the radiation of elastic waves is a straightforward calculation. The model explains an observed scaling relationship between repeat time and seismic moment for repeating seismic events and is consistent with the properties of pseudo-tachylites treated as fossil asperities. Properties of the model are explored with simulations of seismic activity that results when a section of the fault containing a spatial distribution of asperities is subjected to tectonic slip. The simulations show that the failure of a group of strongly interacting asperities satisfies the same scaling relationship as the failure of individual asperities, and that realistic distributions of asperities on a fault plane lead to seismic activity consistent with probability estimates for the interaction of asperities and predicted values of the Gutenberg-Richter a and b values. General features of the model are the exterior crack solution as a theoretical foundation, a heterogeneous state of stress and strength on the fault, dynamic effects controlled by propagating slip pulses and radiated elastic waves with a broad frequency band.

  14. Modeling Users' Experiences with Interactive Systems

    CERN Document Server

    Karapanos, Evangelos

    2013-01-01

    Over the past decade the field of Human-Computer Interaction has evolved from the study of the usability of interactive products towards a more holistic understanding of how they may mediate desired human experiences.  This book identifies the notion of diversity in usersʼ experiences with interactive products and proposes methods and tools for modeling this along two levels: (a) interpersonal diversity in usersʽ responses to early conceptual designs, and (b) the dynamics of usersʼ experiences over time. The Repertory Grid Technique is proposed as an alternative to standardized psychometric scales for modeling interpersonal diversity in usersʼ responses to early concepts in the design process, and new Multi-Dimensional Scaling procedures are introduced for modeling such complex quantitative data. iScale, a tool for the retrospective assessment of usersʼ experiences over time is proposed as an alternative to longitudinal field studies, and a semi-automated technique for the analysis of the elicited exper...

  15. Oil transformation sector modelling: price interactions

    International Nuclear Information System (INIS)

    A global oil and oil product prices evolution model is proposed that covers the transformation sector incidence and the final user price establishment together with price interactions between gaseous and liquid hydrocarbons. High disparities among oil product prices in the various consumer zones (North America, Western Europe, Japan) are well described and compared with the low differences between oil supply prices in these zones. Final user price fluctuations are shown to be induced by transformation differences and competition; natural gas market is also modelled

  16. Strategic Interaction Model with Censored Strategies

    Directory of Open Access Journals (Sweden)

    Nazgul Jenish

    2015-06-01

    Full Text Available In this paper, we develop a new model of a static game of incomplete information with a large number of players. The model has two key distinguishing features. First, the strategies are subject to threshold effects, and can be interpreted as dependent censored random variables. Second, in contrast to most of the existing literature, our inferential theory relies on a large number of players, rather than a large number of independent repetitions of the same game. We establish existence and uniqueness of the pure strategy equilibrium, and prove that the censored equilibrium strategies satisfy a near-epoch dependence property. We then show that the normal maximum likelihood and least squares estimators of this censored model are consistent and asymptotically normal. Our model can be useful in a wide variety of settings, including investment, R&D, labor supply, and social interaction applications.

  17. Simulation of estrogen transport and behavior in laboratory soil columns using a cellular automata model

    Science.gov (United States)

    Chen, Qingcai; Shi, Jianghong; Liu, Xiaowei; Wu, Wei; Liu, Bo; Zhang, Hui

    2013-03-01

    A cellular automata model (CA model) was used to simulate the soil column leaching process of estrogens during the processes of migration and transformation. The results of the simulated leaching experiment showed that the first-order degradation rates of 17α-ethynylestradiol (EE2), 17β-estradiol (E2) and estrone (E1) were 0.131 h- 1 for E2, 0.099 h- 1 for E1 and 0.064 h- 1 for EE2 in the EE2 and E2 leaching process, and the first-order sorption rates were 5.94 h- 1 for E2, 5.63 h- 1 for EE2, 3.125 h- 1 for E1. Their sorption rates were positively correlated with the n-octanol/water partition coefficients. When the diffusion rate was low, its impact on the simulation results was insignificant. The increase in sorption and degradation rates caused the decrease in the total estrogens that leached. In addition, increasing the sorption rate could delay the emerging time of the maximum concentration of estrogen that leached, whereas increasing the degradation rate could shorten the emerging time of the maximum concentration of estrogen that leached. The comparison made between the experimental data and the simulation results of the CA model and the HYDRUS-1D software showed that the establishment of one-component and multi-component CA models could simulate EE2 and E2 soil column leaching processes, and the CA models achieve an intuitive, dynamic, and visual simulation.

  18. Optimal Scaling of Interaction Effects in Generalized Linear Models

    OpenAIRE

    2007-01-01

    Multiplicative interaction models, such as Goodman's RC(M) association models, can be a useful tool for analyzing the content of interaction effects. However, most models for interaction effects are only suitable for data sets with two or three predictor variables. Here, we discuss an optimal scaling model for analyzing the content of interaction effects in generalized linear models with any number of categorical predictor variables. This model, which we call the optimal scaling of interactio...

  19. Optimal Scaling of Interaction Effects in Generalized Linear Models

    OpenAIRE

    van Rosmalen, Joost; Koning, Alex; Groenen, Patrick

    2007-01-01

    textabstractMultiplicative interaction models, such as Goodman's RC(M) association models, can be a useful tool for analyzing the content of interaction effects. However, most models for interaction effects are only suitable for data sets with two or three predictor variables. Here, we discuss an optimal scaling model for analyzing the content of interaction effects in generalized linear models with any number of categorical predictor variables. This model, which we call the optimal scaling o...

  20. Fate of PLA and PCL-Based Polymeric Nanocarriers in Cellular and Animal Models of Triple-Negative Breast Cancer.

    Science.gov (United States)

    Sitia, Leopoldo; Ferrari, Raffaele; Violatto, Martina B; Talamini, Laura; Dragoni, Luca; Colombo, Claudio; Colombo, Laura; Lupi, Monica; Ubezio, Paolo; D'Incalci, Maurizio; Morbidelli, Massimo; Salmona, Mario; Moscatelli, Davide; Bigini, Paolo

    2016-03-14

    An integrated platform to assess the interaction between nanocarriers and biological matrices has been developed by our group using poly methyl-methacrylate nanoparticles. In this study, we exploited this platform to evaluate the behavior of two biodegradable formulations, poly-ε-caprolactone (PCL3) and poly lactic-acid (PLA8), respectively, in cellular and animal models of triple-negative breast cancer (TNBC). Both NPs shared the main physicochemical parameters (size, shape, ζ-potential) and exclusively differentiated on the material on which they are composed. Our results showed that (1) PLA8 NPs, systemically injected in mice, underwent rapid degradation without penetration into tumors; (2) PLA8 NPs were not internalized in the human TNBC cell line (MDA-MB-231); (3) PCL3 NPs had a longer bioavailability, reached the tumor parenchyma, and efficiently penetrated in MDA-MB-231 cells. Our data highlight the relevance of the material selection to both improve bioavailability and target tropism, and make PCL3 NPs an interesting tool for the development of nanodrugs against TNBC. PMID:26791775

  1. Simulation of Regionally Ecological Land Based on a Cellular Automation Model: A Case Study of Beijing, China

    Directory of Open Access Journals (Sweden)

    Xiubin Li

    2012-08-01

    Full Text Available Ecological land is like the “liver” of a city and is very useful to public health. Ecological land change is a spatially dynamic non-linear process under the interaction between natural and anthropogenic factors at different scales. In this study, by setting up natural development scenario, object orientation scenario and ecosystem priority scenario, a Cellular Automation (CA model has been established to simulate the evolution pattern of ecological land in Beijing in the year 2020. Under the natural development scenario, most of ecological land will be replaced by construction land and crop land. But under the scenarios of object orientation and ecosystem priority, the ecological land area will increase, especially under the scenario of ecosystem priority. When considering the factors such as total area of ecological land, loss of key ecological land and spatial patterns of land use, the scenarios from priority to inferiority are ecosystem priority, object orientation and natural development, so future land management policies in Beijing should be focused on conversion of cropland to forest, wetland protection and prohibition of exploitation of natural protection zones, water source areas and forest parks to maintain the safety of the regional ecosystem.

  2. Load-aware modeling for uplink cellular networks in a multi-channel environment

    KAUST Repository

    Alammouri, Ahmad Mohammad Abdel-Karim

    2014-09-01

    We exploit tools from stochastic geometry to develop a tractable analytical approach for modeling uplink cellular networks. The developed model is load aware and accounts for per-user power control as well as the limited transmit power constraint for the users\\' equipment (UEs). The proposed analytical paradigm is based on a simple per-user power control scheme in which each user inverts his path-loss such that the signal is received at his serving base station (BS) with a certain power threshold ρ Due to the limited transmit power of the UEs, users that cannot invert their path-loss to their serving BSs are allowed to transmit with their maximum transmit power. We show that the proposed power control scheme not only provides a balanced cell center and cell edge user performance, it also facilitates the analysis when compared to the state-of-the-art approaches in the literature. To this end, we discuss how to manipulate the design variable ρ in response to the network parameters to optimize one or more of the performance metrics such as the outage probability, the network capacity, and the energy efficiency.

  3. Cellular responses to disruption of the permeability barrier in a three-dimensional organotypic epidermal model

    International Nuclear Information System (INIS)

    Repeated injury to the stratum corneum of mammalian skin (caused by friction, soaps, or organic solvents) elicits hyperkeratosis and epidermal thickening. Functionally, these changes serve to restore the cutaneous barrier and protect the organism. To better understand the molecular and cellular basis of this response, we have engineered an in vitro model of acetone-induced injury using organotypic epidermal cultures. Rat epidermal keratinocytes (REKs), grown on a collagen raft in the absence of any feeder fibroblasts, developed all the hallmarks of a true epidermis including a well-formed cornified layer. To induce barrier injury, REK cultures were treated with intermittent 30-s exposures to acetone then were fixed and paraffin-sectioned. After two exposures, increased proliferation (Ki67 and BrdU staining) was observed in basal and suprabasal layers. After three exposures, proliferation became confined to localized buds in the basal layer and increased terminal differentiation was observed (compact hyperkeratosis of the stratum corneum, elevated levels of K10 and filaggrin, and heightened transglutaminase activity). Thus, barrier disruption causes epidermal hyperplasia and/or enhances differentiation, depending upon the extent and duration of injury. Given that no fibroblasts are present in the model, the ability to mount a hyperplastic response to barrier injury is an inherent property of keratinocytes

  4. Theoretical models and simulation codes to investigate bystander effects and cellular communication at low doses

    Science.gov (United States)

    Ballarini, F.; Alloni, D.; Facoetti, A.; Mairani, A.; Nano, R.; Ottolenghi, A.

    Astronauts in space are continuously exposed to low doses of ionizing radiation from Galactic Cosmic Rays During the last ten years the effects of low radiation doses have been widely re-discussed following a large number of observations on the so-called non targeted effects in particular bystander effects The latter consist of induction of cytogenetic damage in cells not directly traversed by radiation most likely as a response to molecular messengers released by directly irradiated cells Bystander effects which are observed both for lethal endpoints e g clonogenic inactivation and apoptosis and for non-lethal ones e g mutations and neoplastic transformation tend to show non-linear dose responses This might have significant consequences in terms of low-dose risk which is generally calculated on the basis of the Linear No Threshold hypothesis Although the mechanisms underlying bystander effects are still largely unknown it is now clear that two types of cellular communication i e via gap junctions and or release of molecular messengers into the extracellular environment play a fundamental role Theoretical models and simulation codes can be of help in elucidating such mechanisms In the present paper we will review different available modelling approaches including one that is being developed at the University of Pavia The focus will be on the different assumptions adopted by the various authors and on the implications of such assumptions in terms of non-targeted radiobiological damage and more generally low-dose

  5. Detection and Projection of Forest Changes by Using the Markov Chain Model and Cellular Automata

    Directory of Open Access Journals (Sweden)

    Griselda Vázquez-Quintero

    2016-03-01

    Full Text Available The spatio-temporal analysis of land use changes could provide basic information for managing the protection, conservation and production of forestlands, which promotes a sustainable resource use of temperate ecosystems. In this study we modeled and analyzed the spatial and temporal dynamics of land use of a temperate forests in the region of Pueblo Nuevo, Durango, Mexico. Data from the Landsat images Multispectral Scanner (MSS 1973, Thematic Mapper (TM 1990, and Operational Land Imager (OLI 2014 were used. Supervised classification methods were then applied to generate the land use for these years. To validate the land use classifications on the images, the Kappa coefficient was used. The resulting Kappa coefficients were 91%, 92% and 90% for 1973, 1990 and 2014, respectively. The analysis of the change dynamics was assessed with Markov Chains and Cellular Automata (CA, which are based on probabilistic modeling techniques. The Markov Chains and CA show constant changes in land use. The class most affected by these changes is the pine forest. Changes in the extent of temperate forest of the study area were further projected until 2028, indicating that the area of pine forest could be continuously reduced. The results of this study could provide quantitative information, which represents a base for assessing the sustainability in the management of these temperate forest ecosystems and for taking actions to mitigate their degradation.

  6. Tectonic modeling of Konya-Beysehir Region (Turkey using cellular neural networks

    Directory of Open Access Journals (Sweden)

    D. Aydogan

    2007-06-01

    Full Text Available In this paper, to separate regional-residual anomaly maps and to detect borders of buried geological bodies, we applied the Cellular Neural Network (CNN approach to gravity and magnetic anomaly maps. CNN is a stochastic image processing technique, based optimization of templates, which imply relationships of neighborhood pixels in 2-Dimensional (2D potential anomalies. Here, CNN performance in geophysics, tested by various synthetic examples and the results are compared to classical methods such as boundary analysis and second vertical derivatives. After we obtained satisfactory results in synthetic models, we applied CNN to Bouguer anomaly map of Konya-Beysehir Region, which has complex tectonic structure with various fault combinations. We evaluated CNN outputs and 2D/3D models, which are constructed using forward and inversion methods. Then we presented a new tectonic structure of Konya-Beysehir Region. We have denoted (F1, F2, …, F7 and (Konya1, Konya2 faults according to our evaluations of CNN outputs. Thus, we have concluded that CNN is a compromising stochastic image processing technique in geophysics.

  7. Renal Contrast-Enhanced Sonography Findings in a Model of Acute Cellular Allograft Rejection.

    Science.gov (United States)

    Grabner, A; Kentrup, D; Pawelski, H; Mühlmeister, M; Biermann, C; Edemir, B; Heitplatz, B; Van Marck, V; Bettinger, T; Pavenstädt, H; Schlatter, E; Stypmann, J; Tiemann, K; Reuter, S

    2016-05-01

    Noninvasive methods to diagnose and differentiate acute cellular rejection from acute tubular necrosis or acute calcineurin inhibitor toxicity are still missing. Because T lymphocytes play a decisive role in early states of rejection, we investigated the suitability and feasibility of antibody-mediated contrast-enhanced ultrasound by using microbubbles targeted to CD3(+) , CD4(+) , or CD8(+) T cells in different models of renal disease. In an established rat renal transplantation model, CD3-mediated ultrasound allows the detection of acute rejection as early as on postoperative day 2. Ultrasound signal intensities increased with the severity of inflammation. Further, an early response to therapy could be monitored by using contrast-enhanced sonography. Notably, acute tubular necrosis occurring after ischemia-reperfusion injury as well as acute calcineurin inhibitor toxicity could easily be differentiated. Finally, the quantified ultrasound signal correlated significantly with the number of infiltrating T cells obtained by histology and with CD3 mRNA levels, as well as with chemokine CXCL9, CXCL11, and CCL19 mRNA but not with KIM-1 mRNA expression, thereby representing the severity of graft inflammation but not the degree of kidney injury. In summary, we demonstrate that antibody-mediated contrast-enhanced ultrasound targeting T lymphocytes could be a promising tool for an easy and reproducible assessment of acute rejection after renal transplantation. PMID:26613381

  8. Model of Handover and Traffic Based on Cellular Geometry with Smart Antenna

    OpenAIRE

    Zufan Zhang; Jie Zhang; Shaohui Sun

    2014-01-01

    Based on the application of smart antennas in cellular mobile communications, this paper introduces the impact of the width of the antenna beams playing on the dwell time probability density function in cellular geometry with smart antenna. The research results indicate that the smart cell structure can improve the dwell time of users within the cell and improve the traffic system performance.

  9. Cell-centred model for the simulation of curved cellular monolayers

    Science.gov (United States)

    Mosaffa, Payman; Asadipour, Nina; Millán, Daniel; Rodríguez-Ferran, Antonio; J Muñoz, Jose

    2015-12-01

    This paper presents a cell-centred model for the simulation of planar and curved multicellular soft tissues. We propose a computational model that includes stress relaxation due to cell reorganisation (intercellular connectivity changes) and cytoskeleton remodelling (intracellular changes). Cells are represented by their cell centres, and their mechanical interaction is modelled through active non-linear elastic laws with a dynamically changing resting length. Special attention is paid to the handling of connectivity changes between cells, and the relaxation that the tissues exhibit under these topological changes. Cell-cell connectivity is computed by resorting to a Delaunay triangulation, which is combined with a mapping technique in order to obtain triangulations on curved manifolds. Our numerical results show that even a linear elastic cell-cell interaction model may induce a global non-linear response due to the reorganisation of the cell connectivity. This plastic-like behaviour is combined with a non-linear rheological law where the resting length depends on the elastic strain, mimicking the global visco-elastic response of tissues. The model is applied to simulate the elongation of planar and curved monolayers.

  10. The Influence of Receptor-Mediated Interactions on Reaction-Diffusion Mechanisms of Cellular Self-organisation

    KAUST Repository

    Klika, Václav

    2011-11-10

    Understanding the mechanisms governing and regulating self-organisation in the developing embryo is a key challenge that has puzzled and fascinated scientists for decades. Since its conception in 1952 the Turing model has been a paradigm for pattern formation, motivating numerous theoretical and experimental studies, though its verification at the molecular level in biological systems has remained elusive. In this work, we consider the influence of receptor-mediated dynamics within the framework of Turing models, showing how non-diffusing species impact the conditions for the emergence of self-organisation. We illustrate our results within the framework of hair follicle pre-patterning, showing how receptor interaction structures can be constrained by the requirement for patterning, without the need for detailed knowledge of the network dynamics. Finally, in the light of our results, we discuss the ability of such systems to pattern outside the classical limits of the Turing model, and the inherent dangers involved in model reduction. © 2011 Society for Mathematical Biology.

  11. Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.

    Science.gov (United States)

    Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I

    2015-09-01

    Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould. PMID

  12. A Saccharomyces cerevisiae Assay System to Investigate Ligand/AdipoR1 Interactions That Lead to Cellular Signaling

    KAUST Repository

    Aouida, Mustapha

    2013-06-07

    Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both AdipoRs separately. Agonist-AdipoR1 interactions are detected using a split firefly luciferase assay based on reconstitution of firefly luciferase (Luc) activity due to juxtaposition of its N- and C-terminal fragments, NLuc and CLuc, by ligand induced interaction of the chimeric proteins CLuc-AdipoR1 and APPL1-NLuc (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif 1-NLuc) in a S. cerevisiae strain lacking the yeast homolog of AdipoRs (Izh2p). The assay monitors the earliest known step in the adiponectin-AdipoR anti-diabetic signaling cascade. We demonstrate that reconstituted Luc activity can be detected in colonies or cells using a CCD camera and quantified in cell suspensions using a microplate reader. AdipoR1-APPL1 interaction occurs in absence of ligand but can be stimulated specifically by agonists such as adiponectin and the tobacco protein osmotin that was shown to have AdipoR-dependent adiponectin-like biological activity in mammalian cells. To further validate this assay, we have modeled the three dimensional structures of receptor-ligand complexes of membrane-embedded AdipoR1 with cyclic peptides derived from osmotin or osmotin-like plant proteins. We demonstrate that the calculated AdipoR1-peptide binding energies correlate with the peptides\\' ability to behave as AdipoR1 agonists in the split luciferase assay. Further, we demonstrate agonist-AdipoR dependent activation of protein kinase A (PKA) signaling and AMP activated protein kinase (AMPK) phosphorylation in S. cerevisiae, which are homologous to

  13. A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling.

    Directory of Open Access Journals (Sweden)

    Mustapha Aouida

    Full Text Available Adiponectin is a mammalian hormone that exerts anti-diabetic, anti-cancer and cardioprotective effects through interaction with its major ubiquitously expressed plasma membrane localized receptors, AdipoR1 and AdipoR2. Here, we report a Saccharomyces cerevisiae based method for investigating agonist-AdipoR interactions that is amenable for high-throughput scale-up and can be used to study both AdipoRs separately. Agonist-AdipoR1 interactions are detected using a split firefly luciferase assay based on reconstitution of firefly luciferase (Luc activity due to juxtaposition of its N- and C-terminal fragments, NLuc and CLuc, by ligand induced interaction of the chimeric proteins CLuc-AdipoR1 and APPL1-NLuc (adaptor protein containing pleckstrin homology domain, phosphotyrosine binding domain and leucine zipper motif 1-NLuc in a S. cerevisiae strain lacking the yeast homolog of AdipoRs (Izh2p. The assay monitors the earliest known step in the adiponectin-AdipoR anti-diabetic signaling cascade. We demonstrate that reconstituted Luc activity can be detected in colonies or cells using a CCD camera and quantified in cell suspensions using a microplate reader. AdipoR1-APPL1 interaction occurs in absence of ligand but can be stimulated specifically by agonists such as adiponectin and the tobacco protein osmotin that was shown to have AdipoR-dependent adiponectin-like biological activity in mammalian cells. To further validate this assay, we have modeled the three dimensional structures of receptor-ligand complexes of membrane-embedded AdipoR1 with cyclic peptides derived from osmotin or osmotin-like plant proteins. We demonstrate that the calculated AdipoR1-peptide binding energies correlate with the peptides' ability to behave as AdipoR1 agonists in the split luciferase assay. Further, we demonstrate agonist-AdipoR dependent activation of protein kinase A (PKA signaling and AMP activated protein kinase (AMPK phosphorylation in S. cerevisiae, which are

  14. On dark degeneracy and interacting models

    International Nuclear Information System (INIS)

    Cosmological background observations cannot fix the dark energy equation of state, which is related to a degeneracy in the definition of the dark sector components. Here we show that this degeneracy can be broken at perturbation level by imposing two observational properties on dark matter. First, dark matter is defined as the clustering component we observe in large scale structures. This definition is meaningful only if dark energy is unperturbed, which is achieved if we additionally assume, as a second condition, that dark matter is cold, i.e. non-relativistic. As a consequence, dark energy models with equation-of-state parameter −1 ≤ ω < 0 are reduced to two observationally distinguishable classes with ω = −1, equally competitive when tested against observations. The first comprises the ΛCDM model with constant dark energy density. The second consists of interacting models with an energy flux from dark energy to dark matter

  15. Interacting damage models mapped onto ising and percolation models

    Energy Technology Data Exchange (ETDEWEB)

    Toussaint, Renaud; Pride, Steven R.

    2004-03-23

    The authors introduce a class of damage models on regular lattices with isotropic interactions between the broken cells of the lattice. Quasistatic fiber bundles are an example. The interactions are assumed to be weak, in the sense that the stress perturbation from a broken cell is much smaller than the mean stress in the system. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in potential (elastic) energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, they obtain the probability distribution of each damage configuration at any level of the imposed external deformation. They demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, they show that damage models with global load sharing are isomorphic to standard percolation theory, that damage models with local load sharing rule are isomorphic to the standard ising model, and draw consequences thereof for the universality class and behavior of the autocorrelation length of the breakdown transitions corresponding to these models. they also treat damage models having more general power-law interactions, and classify the breakdown process as a function of the power-law interaction exponent. Last, they also show that the probability distribution over configurations is a maximum of Shannon's entropy under some specific constraints related to the energetic balance of the fracture process, which firmly relates this type of quenched-disorder based

  16. Interacting damage models mapped onto Ising and percolation models.

    Science.gov (United States)

    Toussaint, Renaud; Pride, Steven R

    2005-04-01

    We introduce a class of damage models on regular lattices with isotropic interactions between the broken cells of the lattice. Quasi-static fiber bundles are an example. The interactions are assumed to be weak, in the sense that the stress perturbation from a broken cell is much smaller than the mean stress in the system. The system starts intact with a surface-energy threshold required to break any cell sampled from an uncorrelated quenched-disorder distribution. The evolution of this heterogeneous system is ruled by Griffith's principle which states that a cell breaks when the release in potential (elastic) energy in the system exceeds the surface-energy barrier necessary to break the cell. By direct integration over all possible realizations of the quenched disorder, we obtain the probability distribution of each damage configuration at any level of the imposed external deformation. We demonstrate an isomorphism between the distributions so obtained and standard generalized Ising models, in which the coupling constants and effective temperature in the Ising model are functions of the nature of the quenched-disorder distribution and the extent of accumulated damage. In particular, we show that damage models with global load sharing are isomorphic to standard percolation theory and that damage models with a local load sharing rule are isomorphic to the standard Ising model, and draw consequences thereof for the universality class and behavior of the autocorrelation length of the breakdown transitions corresponding to these models. We also treat damage models having more general power-law interactions, and classify the breakdown process as a function of the power-law interaction exponent. Last, we also show that the probability distribution over configurations is a maximum of Shannon's entropy under some specific constraints related to the energetic balance of the fracture process, which firmly relates this type of quenched-disorder based damage model to standard

  17. A cellular stress response (CSR) that interacts with NADPH-P450 reductase (NPR) is a new regulator of hypoxic response.

    Science.gov (United States)

    Oguro, Ami; Koyama, Chika; Xu, Jing; Imaoka, Susumu

    2014-02-28

    NADPH-P450 reductase (NPR) was previously found to contribute to the hypoxic response of cells, but the mechanism was not clarified. In this study, we identified a cellular stress response (CSR) as a new factor interacting with NPR by a yeast two-hybrid system. Overexpression of CSR enhanced the induction of erythropoietin and hypoxia response element (HRE) activity under hypoxia in human hepatocarcinoma cell lines (Hep3B), while knockdown of CSR suppressed them. This new finding regarding the interaction of NPR with CSR provides insight into the function of NPR in hypoxic response. PMID:24491563

  18. Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection

    Directory of Open Access Journals (Sweden)

    Christopher S. Anderson

    2016-01-01

    Full Text Available Systems virology integrates host-directed approaches with molecular profiling to understand viral pathogenesis. Self-contained statistical approaches that combine expression profiles of genes with the available databases defining the genes involved in the pathways (gene-sets have allowed characterization of predictive gene-signatures associated with outcome of the influenza virus (IV infection. However, such enrichment techniques do not take into account interactions among pathways that are responsible for the IV infection pathogenesis. We investigate dendritic cell response to seasonal H1N1 influenza A/New Caledonia/20/1999 (NC infection and infer the Boolean logic rules underlying the interaction network of ligand induced signaling pathways and transcription factors. The model reveals several novel regulatory modes and provides insights into mechanism of cross talk between NFκB and IRF mediated signaling. Additionally, the logic rule underlying the regulation of IL2 pathway that was predicted by the Boolean model was experimentally validated. Thus, the model developed in this paper integrates pathway analysis tools with the dynamic modeling approaches to reveal the regulation between signaling pathways and transcription factors using genome-wide transcriptional profiles measured upon influenza infection.

  19. Analyzing the Influence of Mobile Phone Use of Drivers on Traffic Flow Based on an Improved Cellular Automaton Model

    OpenAIRE

    Yao Xiao; Jing Shi

    2015-01-01

    This paper aimed to analyze the influence of drivers’ behavior of phone use while driving on traffic flow, including both traffic efficiency and traffic safety. An improved cellular automaton model was proposed to simulate traffic flow with distracted drivers based on the Nagel-Schreckenberg model. The driving characters of drivers using a phone were first discussed and a value representing the probability to use a phone while driving was put into the CA model. Simulation results showed that ...

  20. Pairing and realistic shell-model interactions

    OpenAIRE

    Covello, A; Gargano, A.; Kuo, T. T. S.

    2012-01-01

    This paper starts with a brief historical overview of pairing in nuclei, which fulfills the purpose of properly framing the main subject. This concerns the pairing properties of a realistic shell-model effective interaction which has proved very successful in describing nuclei around doubly magic 132Sn. We focus attention on the two nuclei 134Te and 134Sn with two valence protons and neutrons, respectively. Our study brings out the key role of one particle-one hole excitations in producing a ...